I've just downloaded LRTimelapse to experiment with deflickering and exposure grading my time lapse sequences.

I generated a time lapse used 314 jpgs derived from Lightroom using Premiere and it looks great, except for the flicker. So I tried the same thing in LRTimelapse and the order was all funky! It went from no sunlight, to sun, to no sunlight, to sun! I thought it might have been my naming method (I named the files greenacres-1.jpg through greenacres-314.jpg), so I re-exported all of the files so that they were named greenacres-001.jpg through greenacres-314.jpg. The same thing happens. On frame 83 (which corresponds with greenacres-84.jpg) the shot looks more similar to my first frame with no sun, yet when I check the corresponding image in Finder, it looks as it should, with the sun creeping over and partially touching the trees. I have absolutely no idea why LRTimelapse just seems to have the completely wrong idea about what the photo looks like. I cannot replicate it anywhere else.

I'm using Mac OSX 10.4.8.

LRTimelapse uses ExifTool to read the date/time stamps of the images and then sort by date/time regardless of file naming.
Please check that Exiftool is running (message in the main screen) - then check that the Date/Time column in the table is filled, otherwise initialize the sequence. If this doesn't help, play with the checkbox "Sort by Filename". Sometimes turning it on and off resorts the sequence.