I just added this sequence with 1s intervals, and it seems like LRT is adding the first two files in incorrect order. This leads to an issue in LR where the first key frame is the second file. I know these files are potentially <1s apart, but the file stamp sort them in the correct order with 2s difference anyway. See attached.
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LRTimelapse by default sorts by Exif Date. In your case you copied an image to another name, so those two have identical exif dates.
You might switch to filename sorting in LRTimelapse (checkbox above the table), then it will sort alphabetically by filename.
They were indeed two different files, but taken within the same second and had the same exif time stamp, but different file time stamp. I guess this will not be an issue for most.
I'm having an issue now. I've had the wrong files pop up in several spots throughout two separate sequences. This has never happened before. There are multiple files throughout the sequence in LRT (shown as spikes on the curve) that are in the wrong place. In LRT the date/time appears to be correct, but the files are in the wrong place. I cannot choose sort by filename because the filename is already in the correct order. I've included screenshots so you can clearly see the file on my drive is different from what is shown in LRT. The only thing I've done differently is shot with a Nikon D5200 I just bought. Any help would be appreciated.
EDIT: It also just happened with another sequence with a different camera - D7100. So two different cameras and three different memory cards.
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Probably it's only the previews that got messed up: try rebuilding them with Shift-F5 in LRTimelapse.