Hmmm... I can't say as I've ever had this problem (my timelapses, all from Canon DSLRs come in in perfect chronological order). First a workaround and then a question:
Adobe Bridge has a "Batch Rename" function (Tools>>Rename) in which you could rename the files based on their created date. As long as the last thing in the name is the date and time created, it should work (unless you have more than one image taken per second).
If that doesn't work, a couple questions about the camera. Does it name things in chronological order? (e.g. Image_001, Image_002, Image_003 etc?) Also, does it use leading zeroes in the names (Image_001 .... Image_123...etc instead of Image_1...Image_123 etc)?
I use a Canon 6D, I don't have Bridge (or CC or Apeture) tho' I do use Lightroom.
I use PC and Mac and can 'arrange and rename' the files chronologically on both no problem, but AE still seems to pick up from somewhere a different order.
I shot over 1200 timelapse frames recently on the 6D, as you know Canon stores files in folders of 1000, the frames were spread over two folders starting at 9552-9999 on the first folder and from 0001-0846 on the second.
AE creates a video from these files seemingly taking 0001 as the first frame (which is part way through the sequence) then finishes with files from the first 9552 folder.
This is despite the fact I have renamed and can see all files in the correct chron' order on my pc and mac. The files are displayed in the correct chron' order even 'before' renamimg. BTW I usually rename the files on the mac using 'automator'.
> I don't have Bridge
If you have After Effects, you have Bridge. Bridge is installed as part of After Effects CS6 and earlier, and it is available for download for users of After Effects CC.
Really? I didn't know that. I'll check it out.