No clue what's wrong -- insufficient information. But here's a stab in the dark: If you're running AE CC 2015, upen the project file in AE CC 2014; you would be on the cloud, and yu can get it if you don't have it.
There is a point where you run out of layers. It looks like you have reached it. AE can handle a bunch of layers but if you are putting 1000 or more in a single comp I suspect that you may be trying to edit more than a shot or a short sequence in AE. That's not a practical workflow.
If you are working on a shot that has more than 1000 elements then it's probably a good idea to group them into sections (pre-comps) then nest the sections together to edit the final shot.
Thanks Dave for responding. I think I found the answer in the a creative cow thread. After Effects can't, doesn't, won't display the layers viewable trim sections past a certain number.
Thanks for the response. I found this same thing in a Creative Cow article. That's what I did, I used pre-comps to group the word art into manageable chunks. I realize it wasn't a practical workflow, but made sense to me at the time.
It's not exactly that you "run out of layers". The layers are still there (i.e., their images should show up in the Composition panel). The bug is that the Timeline panel can't draw the representations of that many layers in list view. The limit is ~30,000 pixels of vertical height; since each layer takes a little more than 20 pixels vertically in the Timeline panel, that works out to somewhere between 1,000 and 2,000 layers to trigger the problem.
To fix this bug requires rewriting how we draw list views. This is not the highest priority right now because typical compositions don't have that many layers, and the ones that do tend to use precompositions to manage them.
If this is getting in your way, you can influence the priority of fixing this bug by submitting a report here: