I did a quick search and couldn't find this problem posted anywhere.
I've had this problem a number of times in AE CS4. I don't get an error and can't figure out what the problem is.
I'm using layered illustrator files and every once in a while, After Effects will read the layers as either empty or strangely cropped. Again, no error message, but something about the exchange is clearly off. Doing a footage reload doesn't fix it either, I have to do a replace footage and re-import the layer to clear things up.
Anybody else have this issue? It's pretty frustrating when you look at your rendered QT and there are big holes in the animation!
I think I understand part of the problems your experiencing. I'm still back with AI 10 but I'm sure the principles are still the same.
When I create an Illustrator file that with be used in AE, I set the Document Setup settings to correspond to the AE comp that's to be used. Most importantly, I then immediately create a new layer in AI (and keep it the lowest as you work), use the Make Crop Marks tool, then Release. This creates the bounding box that AE will use to set the layer dims later when you import.
Although I'll work in AI with a stroke color, I often set it to None before exporting and have just a solid Fill color.
AE only sees the highest level of an AI layer so when you import it'll be like Flattening Artwork for each layer. If you need to have a particular layer in AI as a layer in AE, you'll have to move it up to to a highest level layer in AI first.
When importing into AE, use Import As: Composition rather than footage or cropped layers. The bounding box you created in AI will set the subsequently created AE comp and it's layers to the dims you set up to begin with.