I have a camera that makes time-lapse photographs and I've been using AE v.5.5 (ancient, I know) successfully for the last few weeks to turn these sequences into QT movies. I do Import>File>JPEG Import as Footage and click the JPEG sequence box. As of date, I've made 6 different movies this way - the frames are numbered sequentially, starting at 1 and continuing until, typically, between 1,300 and 1,500 images. Again, no problem until today. I did the exact same thing (many times) with a new sequences, but it only imports frames 1-999. The sequences is 1,440 frames, but it just refuses to Import the entire sequence, always stopping at 999. I've checked preferences though find nothing that would seem to effect that and, besides, it has been importing longer sequences without a problem until now.
What can I do? Is there something to check for that might be creating a sort of Upper-limit on how large a sequence AE will import?
What is the file name? That is the first place to look. File names like anim_00001.jpg should work but file names like anim_001.jpg may only show up as 999 frames.
As Rick said, check the numbering. In ancient versions of AE there were limitations on that like e.g. not correctly handling UNIX-style numbering as Maya would produce it in its default settings (file.1.jp to file.9999.jpg for instance). Unpadded numbers can severely throw AE off track....