Layers in my composition is not sequential. After 999 the layer numbers begin at 100 and then oddly enough each layer in the time line is the same for each layer. In other words, there are many duplicates in the composition. Any suggestions as to why? How come all separate layers are not different numbers?
First question, why so many layers? Making changes to a comp like that would be insane. AE is designed to create shots and short sequences. It is one of the worst tools to use to edit a movie.
The first thing I would check is the column width of layer number in the timeline. If that doesn't fix the problem let us know.
By the way, if you are generating that many layers because you are sequencing images for a time lapse is much better and more efficient way to do that. Just import the image sequence as an image sequence and it comes in like a movie.