I'm having the same problem. The rendered video has about 960 of 5600 images.
The Path to MPEG Encoder is set to: C:\Program Files (x86)\LRTimelapse 3\ffmpeg64.exe
Here's the logfile for this sequence:
[2014-04-21 17:23:07] DEBUG: Found render tasks!
[2014-04-21 17:23:07] DEBUG: Launching render Task: A:\Tim's Photos\2014\2014 AK MOM\20140410 Treatment Day 1 Time Lapse\20140410 Xray Triage Areas Time Lapse\LRT_20140410_Xray_Triage_Areas_Time_Lapse
[2014-04-21 17:23:07] DEBUG: Launching mpeg converter: C:\Program Files (x86)\LRTimelapse 3\ffmpeg64.exe
[2014-04-21 17:23:07] DEBUG: Rendering in 1920x1280
[2014-04-21 17:23:08] DEBUG: Launched encoder.
[2014-04-21 17:23:08] DEBUG: Speed 1.0
[2014-04-21 17:23:08] DEBUG: Quality 2
[2014-04-21 17:23:08] DEBUG: Frame rate 29.97
[2014-04-21 17:23:08] DEBUG: Output cs 420
[2014-04-21 17:23:09] DEBUG: ffmpeg version N-57287-g712eff4 Copyright © 2000-2013 the FFmpeg developers
[2014-04-21 17:23:09] DEBUG: built on Oct 20 2013 20:00:08 with gcc 4.8.2 (GCC)
[2014-04-21 17:23:09] 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-libcaca --enable-libfreetype --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-libx264 --enable-libxavs --enable-libxvid --enable-zlib
[2014-04-21 17:23:09] DEBUG: libavutil 52. 47.101 / 52. 47.101
[2014-04-21 17:23:09] DEBUG: libavcodec 55. 37.102 / 55. 37.102
[2014-04-21 17:23:09] DEBUG: libavformat 55. 19.103 / 55. 19.103
[2014-04-21 17:23:09] DEBUG: libavdevice 55. 4.100 / 55. 4.100
[2014-04-21 17:23:09] DEBUG: libavfilter 3. 88.102 / 3. 88.102
[2014-04-21 17:23:09] DEBUG: libswscale 2. 5.101 / 2. 5.101
[2014-04-21 17:23:09] DEBUG: libswresample 0. 17.104 / 0. 17.104
[2014-04-21 17:23:09] DEBUG: libpostproc 52. 3.100 / 52. 3.100
[2014-04-21 17:23:09] DEBUG: Input #0, image2, from 'A:\Tim's Photos\2014\2014 AK MOM\20140410 Treatment Day 1 Time Lapse\20140410 Xray Triage Areas Time Lapse\LRT_20140410_Xray_Triage_Areas_Time_Lapse\LRT_%05d.jpg':
[2014-04-21 17:23:09] DEBUG: Duration: 00:00:59.44, start: 0.000000, bitrate: N/A
[2014-04-21 17:23:09] DEBUG: Stream #0:0: Video: mjpeg, yuvj444p(pc), 4096x2731, 25 tbr, 25 tbn, 25 tbc
[2014-04-21 17:23:09] DEBUG: [swscaler @ 00000000026cd5e0] deprecated pixel format used, make sure you did set range correctly
[2014-04-21 17:23:09] DEBUG: [libx264 @ 00000000026a8c80] using cpu capabilities: MMX2 SSE2Fast SSSE3 SSE4.2
[2014-04-21 17:23:09] DEBUG: [libx264 @ 00000000026a8c80] profile High, level 4.0
[2014-04-21 17:23:09] DEBUG: [libx264 @ 00000000026a8c80] 264 - core 138 r2358 9e941d1 - H.264/MPEG-4 AVC codec - Copyleft 2003-2013 -
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=25 scenecut=40 intra_refresh=0 rc_lookahead=40 rc=crf mbtree=1 crf=16.0 qcomp=0.60 qpmin=0 qpmax=69 qpstep=4 ip_ratio=1.40 aq=1:1.00
[2014-04-21 17:23:09] DEBUG: Output #0, mp4, to 'C:\Users\Tim\AppData\Local\Temp\LRT_Render_9111847140516633022.mp4':
[2014-04-21 17:23:09] DEBUG: Metadata:
[2014-04-21 17:23:09] DEBUG: creation_time : 2014-04-21T17:23:07
[2014-04-21 17:23:09] DEBUG: encoder : Lavf55.19.103
[2014-04-21 17:23:09] DEBUG: Stream #0:0: Video: h264 (libx264) ([33][0][0][0] / 0x0021), yuv420p, 1920x1080, q=-1--1, 11988 tbn, 29.97 tbc
[2014-04-21 17:23:09] DEBUG: Stream mapping:
[2014-04-21 17:23:09] DEBUG: Stream #0:0 (mjpeg) -> scale
[2014-04-21 17:23:09] DEBUG: unsharp -> Stream #0:0 (libx264)
[2014-04-21 17:23:09] DEBUG: Press [q] to stop, [?] for help
[2014-04-21 17:25:36] DEBUG: Loading A:\Tim's Photos\2014\2014 AK MOM\20140410 Treatment Day 1 Time Lapse\20140410 Treatment Area Time Lapse
[2014-04-21 17:25:55] DEBUG: Loading A:\Tim's Photos\2014\2014 AK MOM\20140410 Treatment Day 1 Time Lapse\20140410 Xray Triage Areas Time Lapse\LRT_20140410_Xray_Triage_Areas_Time_Lapse
[2014-04-21 17:25:55] DEBUG: jpg sequence found.
[2014-04-21 17:30:22] DEBUG:
[2014-04-21 17:30:22] DEBUG: video:184236kB audio:0kB subtitle:0 global headers:0kB muxing overhead 0.010803%
[2014-04-21 17:30:22] DEBUG: [libx264 @ 00000000026a8c80] frame I:6 Avg QP:16.78 size:499649
[2014-04-21 17:30:22] DEBUG: [libx264 @ 00000000026a8c80] frame P:743 Avg QP:19.26 size:159414
[2014-04-21 17:30:22] DEBUG: [libx264 @ 00000000026a8c80] frame B:737 Avg QP:22.16 size: 91200
[2014-04-21 17:30:22] DEBUG: [libx264 @ 00000000026a8c80] consecutive B-frames: 0.8% 99.2% 0.0% 0.0%
[2014-04-21 17:30:22] DEBUG: [libx264 @ 00000000026a8c80] mb I I16..4: 2.1% 62.7% 35.2%
[2014-04-21 17:30:22] DEBUG: [libx264 @ 00000000026a8c80] mb P I16..4: 0.2% 6.6% 4.7% P16..4: 39.6% 25.5% 20.0% 0.0% 0.0% skip: 3.4%
[2014-04-21 17:30:22] DEBUG: [libx264 @ 00000000026a8c80] mb B I16..4: 0.1% 2.8% 3.4% B16..8: 32.7% 15.0% 7.8% direct:11.2% skip:27.0% L0:53.3% L1:34.4% BI:12.3%
[2014-04-21 17:30:22] DEBUG: [libx264 @ 00000000026a8c80] 8x8 transform intra:53.5% inter:55.4%
[2014-04-21 17:30:22] DEBUG: [libx264 @ 00000000026a8c80] coded y,uvDC,uvAC intra: 97.0% 96.0% 84.3% inter: 52.5% 59.0% 13.0%
[2014-04-21 17:30:22] DEBUG: [libx264 @ 00000000026a8c80] i16 v,h,dc,p: 25% 3% 4% 68%
[2014-04-21 17:30:22] DEBUG: [libx264 @ 00000000026a8c80] i8 v,h,dc,ddl,ddr,vr,hd,vl,hu: 26% 11% 10% 5% 8% 11% 8% 9% 11%
[2014-04-21 17:30:22] DEBUG: [libx264 @ 00000000026a8c80] i4 v,h,dc,ddl,ddr,vr,hd,vl,hu: 23% 13% 8% 6% 10% 13% 9% 9% 10%
[2014-04-21 17:30:22] DEBUG: [libx264 @ 00000000026a8c80] i8c dc,h,v,p: 41% 17% 30% 12%
[2014-04-21 17:30:22] DEBUG: [libx264 @ 00000000026a8c80] Weighted P-Frames: Y:13.2% UV:3.2%
[2014-04-21 17:30:22] DEBUG: [libx264 @ 00000000026a8c80] ref P L0: 36.8% 18.0% 24.1% 18.7% 2.4%
[2014-04-21 17:30:22] DEBUG: [libx264 @ 00000000026a8c80] ref B L0: 57.6% 42.4%
[2014-04-21 17:30:22] DEBUG: [libx264 @ 00000000026a8c80] kb/s:30438.97
[2014-04-21 17:30:22] DEBUG: External encoder finished successfully.
[2014-04-21 17:30:24] INFO: Copied temporary file to render directory.
[2014-04-21 17:30:24] INFO: ...deleted temporary file.
[2014-04-21 17:30:24] INFO: Rendered video is located at: A:\Tim's Photos\2014\2014 AK MOM\20140410 Treatment Day 1 Time Lapse\20140410 Xray Triage Areas Time Lapse\20140410_Xray_Triage_Areas_Time_Lapse_h264-420_1080p_HQ.mp4
[2014-04-21 17:30:24] DEBUG: Launching mpeg converter: C:\Program Files (x86)\LRTimelapse 3\ffmpeg64.exe
[2014-04-21 17:30:24] DEBUG: Rendering in 1920x1280
[2014-04-21 17:30:24] INFO: Deleted existing file.
[2014-04-21 17:30:24] DEBUG: Launched encoder.
[2014-04-21 17:30:24] DEBUG: Speed 1.0
[2014-04-21 17:30:24] DEBUG: Quality 2
[2014-04-21 17:30:24] DEBUG: Frame rate 29.97
[2014-04-21 17:30:24] DEBUG: Output cs 420
[2014-04-21 17:30:25] DEBUG: ffmpeg version N-57287-g712eff4 Copyright © 2000-2013 the FFmpeg developers
[2014-04-21 17:30:25] DEBUG: built on Oct 20 2013 20:00:08 with gcc 4.8.2 (GCC)
[2014-04-21 17:30:25] 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-libcaca --enable-libfreetype --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-libx264 --enable-libxavs --enable-libxvid --enable-zlib
[2014-04-21 17:30:25] DEBUG: libavutil 52. 47.101 / 52. 47.101
[2014-04-21 17:30:25] DEBUG: libavcodec 55. 37.102 / 55. 37.102
[2014-04-21 17:30:25] DEBUG: libavformat 55. 19.103 / 55. 19.103
[2014-04-21 17:30:25] DEBUG: libavdevice 55. 4.100 / 55. 4.100
[2014-04-21 17:30:25] DEBUG: libavfilter 3. 88.102 / 3. 88.102
[2014-04-21 17:30:25] DEBUG: libswscale 2. 5.101 / 2. 5.101
[2014-04-21 17:30:25] DEBUG: libswresample 0. 17.104 / 0. 17.104
[2014-04-21 17:30:25] DEBUG: libpostproc 52. 3.100 / 52. 3.100
[2014-04-21 17:30:25] DEBUG: Input #0, image2, from 'A:\Tim's Photos\2014\2014 AK MOM\20140410 Treatment Day 1 Time Lapse\20140410 Xray Triage Areas Time Lapse\LRT_20140410_Xray_Triage_Areas_Time_Lapse\LRT_%05d.jpg':
[2014-04-21 17:30:25] DEBUG: Duration: 00:00:59.44, start: 0.000000, bitrate: N/A
[2014-04-21 17:30:25] DEBUG: Stream #0:0: Video: mjpeg, yuvj444p(pc), 4096x2731, 25 tbr, 25 tbn, 25 tbc
[2014-04-21 17:30:25] DEBUG: [swscaler @ 0000000000346420] deprecated pixel format used, make sure you did set range correctly
[2014-04-21 17:30:25] DEBUG: [libx264 @ 0000000000338b00] using cpu capabilities: MMX2 SSE2Fast SSSE3 SSE4.2
[2014-04-21 17:30:25] DEBUG: [libx264 @ 0000000000338b00] profile High, level 5.0
[2014-04-21 17:30:25] DEBUG: [libx264 @ 0000000000338b00] 264 - core 138 r2358 9e941d1 - H.264/MPEG-4 AVC codec - Copyleft 2003-2013 -
http://www.videolan.org/x264.html - options: cabac=1 ref=3 deblock=1:0:0