I have 3 time lapse sequences that I'm working with, all 3 were shot the same morning during a sunrise.

Since I do not care for having a water mark in the middle of the video using the Pro version, I did an initial export from LR using the LRT plugin for all 3 sequences. I then re-exported those results into another folder using LR so that I could add my copyright logo.  I rendered the video sequences from the images with my copyright. 

Sequence A has 590 images, but only about 300 of the images were rendered into the video.

Sequence B has 700 images, but only about 400 of the images were rendered into the video.

Sequence C has 190 images and it was rendered correctly.

I have not had problems rendering other videos using the normal work flow.  

Any ideas on what to do?

If the render does not render the whole sequence, please check the log file (info-menu/show log) maybe this is your problem:
http://forum.lrtimelapse.com/Thread-rend...e-sequence

Otherwise I have no idea and cannot give support if you don't use the LRTExport plugin, I hope you understand that.

Thanks for the speedy response.

I did look at the thread that your referenced before posting this. I have not done any cropping or changing of the aspect ratio with any of the 3 sequences. 

I did close LRTL, LR and power off my computer. I have an older PC and at times that resolves odd problems. But no luck this time. I just tried to render a video of the jpgs using LRTL and it stopped at frame 287 of 590. 

Support request from Timothy Grams, tim grams photography, Anchorage, EMail: trgrams712@gmail.com
License for: LRTimelapse 4, License type: professional, Payment reference: , Valid until: Lifetime

[2015-12-10 07:52:27] INFO: Log file was created at C:\Users\Tim\AppData\Roaming\LRTimelapse\LRTimelapse.log
[2015-12-10 07:52:28] DEBUG: Loading properties from C:\Users\Tim\AppData\Roaming\LRTimelapse\user.props
[2015-12-10 07:52:28] INFO: LRTimelapse 4.4 (2015-10-05) Build 91
[2015-12-10 07:52:28] INFO: © 2015 Gunther Wegner
[2015-12-10 07:52:28] INFO: http://lrtimelapse.com
[2015-12-10 07:52:28] INFO: Java version: 1.8.0_66 (64bit) from Oracle Corporation
[2015-12-10 07:52:28] INFO: Running on: Windows 7 locale: en_US
[2015-12-10 07:52:28] INFO: Windows architecture: 64 bit
[2015-12-10 07:52:28] INFO: Java runtime: 64 bit
[2015-12-10 07:52:28] INFO: ------------------------------------
[2015-12-10 07:52:29] INFO: Licensed to: Timothy Grams, tim grams photography, Anchorage - Professional License.
[2015-12-10 07:52:30] INFO: Using W7/W8 task bar extensions.
[2015-12-10 07:52:30] DEBUG: Initializing directory chooser.
[2015-12-10 07:52:31] INFO: Done (dirchooser)...
[2015-12-10 07:52:33] DEBUG: Launching ExifTool: C:\Program Files (x86)\LRTimelapse 4\exiftool.exe
[2015-12-10 07:52:34] INFO: ExifTool: 10.02 {ready}
[2015-12-10 07:52:34] DEBUG: Exif Tool available.
[2015-12-10 07:52:34] DEBUG: DNG Converter available.
[2015-12-10 07:52:34] DEBUG: MPEG Encoder available.
[2015-12-10 07:52:34] INFO: Detected Screen size: 2560 x 1440
[2015-12-10 07:52:35] INFO: Latest version: 4.4 (2015-10-05), current Version: 4.4 (2015-10-05)
[2015-12-10 08:05:16] INFO: --- Loading directory: Q:\Tims Photos\Time Lapse Sequences\2015\20151206 Crow Creek Pass Trailhead A\Jpegs with CR
[2015-12-10 08:05:26] DEBUG: Memory: [max|10183] [used|729] [free|9454]
[2015-12-10 08:05:26] DEBUG: Loading sequence properties from Q:\Tims Photos\Time Lapse Sequences\2015\20151206 Crow Creek Pass Trailhead A\Jpegs with CR\.lrt\lrtsequence.properties
[2015-12-10 08:05:26] WARN: Properties-file not found.
[2015-12-10 08:05:26] DEBUG: Buffer size for ExifTool: 59
[2015-12-10 08:05:26] DEBUG: Sequence shot in manual mode
[2015-12-10 08:05:26] DEBUG: Timestamp Data complete!
[2015-12-10 08:05:26] DEBUG: Sequence is new or was processed with LRT < 4.0
[2015-12-10 08:06:11] DEBUG: Done loading previews.
[2015-12-10 08:06:11] DEBUG: Memory: [max|10183] [used|712] [free|9471]
[2015-12-10 08:09:05] WARN: Forgot to apply deflicker?
[2015-12-10 08:09:54] INFO: 590 XMP-files successfully saved.
[2015-12-10 08:13:43] DEBUG: Loading Q:\Tims Photos\Time Lapse Sequences\2015\20151206 Crow Creek Pass Trailhead A\Jpegs with CR
[2015-12-10 08:13:43] DEBUG: jpg sequence found.
[2015-12-10 08:13:43] DEBUG: Dimensions: 4096 x 2731
[2015-12-10 08:13:59] DEBUG: Launching mpeg converter: C:\Program Files (x86)\LRTimelapse 4\ffmpeg64.exe
[2015-12-10 08:13:59] INFO: Deleted existing file.
[2015-12-10 08:13:59] DEBUG: Launched encoder.
[2015-12-10 08:13:59] DEBUG:   Speed 1.0
[2015-12-10 08:13:59] DEBUG:   Quality 0
[2015-12-10 08:13:59] DEBUG:   Frame rate 23.976
[2015-12-10 08:13:59] DEBUG:   Output cs 420
[2015-12-10 08:13:59] DEBUG:   Width 1280
[2015-12-10 08:13:59] DEBUG:   Height 856
[2015-12-10 08:14:00] DEBUG: ffmpeg version N-71095-gdf43d03 Copyright © 2000-2015 the FFmpeg developers
[2015-12-10 08:14:00] DEBUG:   built with gcc 4.9.2 (GCC)
[2015-12-10 08:14:00] DEBUG:   configuration: --enable-gpl --enable-version3 --disable-w32threads --enable-avisynth --enable-bzlib --enable-fontconfig --enable-frei0r --enable-gnutls --enable-iconv --enable-libass --enable-libbluray --enable-libbs2b --enable-libcaca --enable-libfreetype --enable-libgme --enable-libgsm --enable-libilbc --enable-libmodplug --enable-libmp3lame --enable-libopencore-amrnb --enable-libopencore-amrwb --enable-libopenjpeg --enable-libopus --enable-librtmp --enable-libschroedinger --enable-libsoxr --enable-libspeex --enable-libtheora --enable-libtwolame --enable-libvidstab --enable-libvo-aacenc --enable-libvo-amrwbenc --enable-libvorbis --enable-libvpx --enable-libwavpack --enable-libwebp --enable-libx264 --enable-libx265 --enable-libxavs --enable-libxvid --enable-lzma --enable-decklink --enable-zlib
[2015-12-10 08:14:00] DEBUG:   libavutil      54. 20.101 / 54. 20.101
[2015-12-10 08:14:00] DEBUG:   libavcodec     56. 30.100 / 56. 30.100
[2015-12-10 08:14:00] DEBUG:   libavformat    56. 26.101 / 56. 26.101
[2015-12-10 08:14:00] DEBUG:   libavdevice    56.  4.100 / 56.  4.100
[2015-12-10 08:14:00] DEBUG:   libavfilter     5. 13.101 /  5. 13.101
[2015-12-10 08:14:00] DEBUG:   libswscale      3.  1.101 /  3.  1.101
[2015-12-10 08:14:00] DEBUG:   libswresample   1.  1.100 /  1.  1.100
[2015-12-10 08:14:00] DEBUG:   libpostproc    53.  3.100 / 53.  3.100
[2015-12-10 08:14:00] DEBUG: Input #0, image2, from 'Q:\Tims Photos\Time Lapse Sequences\2015\20151206 Crow Creek Pass Trailhead A\Jpegs with CR\LRT_%05d.jpg':
[2015-12-10 08:14:00] DEBUG:   Duration: 00:00:23.60, start: 0.000000, bitrate: N/A
[2015-12-10 08:14:00] DEBUG:     Stream #0:0: Video: mjpeg, yuvj444p(pc, bt470bg/unknown/unknown), 4096x2731, 25 fps, 25 tbr, 25 tbn, 25 tbc
[2015-12-10 08:14:00] DEBUG: [swscaler @ 0000000002c67c80] deprecated pixel format used, make sure you did set range correctly
[2015-12-10 08:14:00] DEBUG: [libx264 @ 0000000002c715c0] using cpu capabilities: MMX2 SSE2Fast SSSE3 SSE4.2
[2015-12-10 08:14:00] DEBUG: [libx264 @ 0000000002c715c0] profile High, level 4.0
[2015-12-10 08:14:00] DEBUG: [libx264 @ 0000000002c715c0] 264 - core 146 r2538 121396c - H.264/MPEG-4 AVC codec - Copyleft 2003-2015 - http://www.videolan.org/x264.html - options: cabac=1 ref=3 deblock=1:0:0 analyse=0x3:0x113 me=hex subme=7 psy=1 psy_rd=1.00:0.00 mixed_ref=1 me_range=16 chroma_me=1 trellis=1 8x8dct=1 cqm=0 deadzone=21,11 fast_pskip=1 chroma_qp_offset=-2 threads=12 lookahead_threads=2 sliced_threads=0 nr=0 decimate=1 interlaced=0 bluray_compat=0 constrained_intra=0 bframes=3 b_pyramid=2 b_adapt=1 b_bias=0 direct=1 weightb=1 open_gop=0 weightp=2 keyint=250 keyint_min=23 scenecut=40 intra_refresh=0 rc_lookahead=40 rc=abr mbtree=1 bitrate=20000 ratetol=1.0 qcomp=0.60 qpmin=0 qpmax=69 qpstep=4 ip_ratio=1.40 aq=1:1.00
[2015-12-10 08:14:00] DEBUG: Output #0, mp4, to 'C:\Users\Tim\AppData\Local\Temp\LRT_Render_4190933229298192871.mp4':
[2015-12-10 08:14:00] DEBUG:   Metadata:
[2015-12-10 08:14:00] DEBUG:     creation_time   : 2015-12-10T08:13:59
[2015-12-10 08:14:00] DEBUG:     encoder         : Lavf56.26.101
[2015-12-10 08:14:00] DEBUG:     Stream #0:0: Video: h264 (libx264) ([33][0][0][0] / 0x0021), yuv420p, 1280x856, q=-1--1, 20000 kb/s, 23.98 fps, 11988 tbn, 23.98 tbc
[2015-12-10 08:14:00] DEBUG:     Metadata:
[2015-12-10 08:14:00] DEBUG:       encoder         : Lavc56.30.100 libx264
[2015-12-10 08:14:00] DEBUG: Stream mapping:
[2015-12-10 08:14:00] DEBUG:   Stream #0:0 (mjpeg) -> scale
[2015-12-10 08:14:00] DEBUG:   unsharp -> Stream #0:0 (libx264)
[2015-12-10 08:14:00] DEBUG: Press [q] to stop, [?] for help
[2015-12-10 08:14:01] DEBUG: Input stream #0:0 frame changed from size:4096x2731 fmt:yuvj444p to size:4096x2731 fmt:yuvj420p
[2015-12-10 08:14:01] DEBUG: [swscaler @ 0000000002c7fda0] deprecated pixel format used, make sure you did set range correctly
[2015-12-10 08:14:01] DEBUG: [swscaler @ 0000000002cbcea0] deprecated pixel format used, make sure you did set range correctly
[2015-12-10 08:14:21] DEBUG: Input stream #0:0 frame changed from size:4096x2731 fmt:yuvj420p to size:4096x2731 fmt:yuvj444p
[2015-12-10 08:14:21] DEBUG: [swscaler @ 0000000002cd50a0] deprecated pixel format used, make sure you did set range correctly
[2015-12-10 08:14:21] DEBUG: [swscaler @ 0000000002caece0] deprecated pixel format used, make sure you did set range correctly
[2015-12-10 08:14:24] DEBUG: Input stream #0:0 frame changed from size:4096x2731 fmt:yuvj444p to size:4096x2731 fmt:yuvj420p
[2015-12-10 08:14:24] DEBUG: [swscaler @ 0000000002cd50a0] deprecated pixel format used, make sure you did set range correctly
[2015-12-10 08:14:24] DEBUG: [swscaler @ 00000000049e4680] deprecated pixel format used, make sure you did set range correctly
[2015-12-10 08:14:40] DEBUG: video:29838kB audio:0kB subtitle:0kB other streams:0kB global headers:0kB muxing overhead: 0.014931%
[2015-12-10 08:14:40] DEBUG: [libx264 @ 0000000002c715c0] frame I:2     Avg QP: 3.61  size:335776
[2015-12-10 08:14:40] DEBUG: [libx264 @ 0000000002c715c0] frame P:132   Avg QP: 8.82  size:145526
[2015-12-10 08:14:40] DEBUG: [libx264 @ 0000000002c715c0] frame B:153   Avg QP:10.60  size: 69753
[2015-12-10 08:14:40] DEBUG: [libx264 @ 0000000002c715c0] consecutive B-frames:  7.3% 55.1% 29.3%  8.4%
[2015-12-10 08:14:40] DEBUG: [libx264 @ 0000000002c715c0] mb I  I16..4: 20.5% 25.1% 54.3%
[2015-12-10 08:14:40] DEBUG: [libx264 @ 0000000002c715c0] mb P  I16..4:  6.3% 18.2% 11.1%  P16..4: 23.7% 23.0% 17.4%  0.0%  0.0%    skip: 0.3%
[2015-12-10 08:14:40] DEBUG: [libx264 @ 0000000002c715c0] mb B  I16..4:  2.4%  3.1%  2.1%  B16..8: 29.4% 20.8%  9.2%  direct:24.2%  skip: 8.7%  L0:40.6% L1:34.1% BI:25.3%
[2015-12-10 08:14:40] DEBUG: [libx264 @ 0000000002c715c0] final ratefactor: 9.58
[2015-12-10 08:14:40] DEBUG: [libx264 @ 0000000002c715c0] 8x8 transform intra:48.2% inter:33.6%
[2015-12-10 08:14:40] DEBUG: [libx264 @ 0000000002c715c0] coded y,uvDC,uvAC intra: 84.1% 68.2% 65.8% inter: 72.5% 60.0% 36.8%
[2015-12-10 08:14:40] DEBUG: [libx264 @ 0000000002c715c0] i16 v,h,dc,p:  6% 61% 12% 21%
[2015-12-10 08:14:40] DEBUG: [libx264 @ 0000000002c715c0] i8 v,h,dc,ddl,ddr,vr,hd,vl,hu:  6% 52% 19%  2%  4%  2%  7%  2%  6%
[2015-12-10 08:14:40] DEBUG: [libx264 @ 0000000002c715c0] i4 v,h,dc,ddl,ddr,vr,hd,vl,hu: 15% 42% 19%  3%  6%  2%  6%  2%  5%
[2015-12-10 08:14:40] DEBUG: [libx264 @ 0000000002c715c0] i8c dc,h,v,p: 51% 41%  5%  3%
[2015-12-10 08:14:40] DEBUG: [libx264 @ 0000000002c715c0] Weighted P-Frames: Y:27.3% UV:15.9%
[2015-12-10 08:14:40] DEBUG: [libx264 @ 0000000002c715c0] ref P L0: 56.4%  9.0% 20.4% 11.8%  2.5%
[2015-12-10 08:14:40] DEBUG: [libx264 @ 0000000002c715c0] ref B L0: 67.3% 29.8%  2.9%
[2015-12-10 08:14:40] DEBUG: [libx264 @ 0000000002c715c0] ref B L1: 89.7% 10.3%
[2015-12-10 08:14:40] DEBUG: [libx264 @ 0000000002c715c0] kb/s:20419.31
[2015-12-10 08:14:40] DEBUG: External encoder finished successfully.
[2015-12-10 08:14:40] INFO: Copied temporary file to render directory.
[2015-12-10 08:14:40] INFO: ...deleted temporary file.
[2015-12-10 08:14:40] INFO: Rendered video is located at: Q:\Tims Photos\Time Lapse Sequences\2015\20151206 Crow Creek Pass Trailhead A\Jpegs with CR_h264-420_720p_23.976_LQ.mp4
[2015-12-10 08:14:41] DEBUG: Locating in Explorer: Q:\Tims Photos\Time Lapse Sequences\2015\20151206 Crow Creek Pass Trailhead A\Jpegs with CR_h264-420_720p_23.976_LQ.mp4

So, if I understand you right, you edited the intermediary sequences (jpgs exported by LRTExport) in a pixel based editor to add your logo. Obviously when saving them, the software you used to add the logo, changed the color format, so that they caused problems to the video renderer.
I'd suggest you add your logo, when composing the final video from the single sequences you did with LRTimelapse in the video editing program. This is much easier and the way to go. The LRTimelapse original clips are better to be left without any logo, just in case you want to use them for something else sometimes. Adding a logo layer in a video editor is a piece of cake.

I did the Holy Grail work flow on raw files. Then I used Lightroom to export intermediary jpegs using the LTRL menu. I used LR to export those intermediary jpegs into another folder and added my logo in that export process. Other than adding my logo, I did not make any changes to the jpegs. I then opened that folder in LR TimeLapse. I did not do any editing. I rendered the video using the intermediary jpegs that had my logo.

I will use an video editing program to add my logo.

As always, thanks for the speedy assistance and a super program!