I'm in a project that originated in Premiere with a lot of footage layers, working in 29.97 DF across all my comps. AE 2015.3 (220.127.116.11), OS X 10.10.5.
Things started out fine, but I after precomposing a large group of layers together, I'm seeing the precomp and a number of layers within it are both off by a fraction of a frame. That is, I can zoom in right down to frame level, but I'll see the in point of a layer inside or outside the frame by just a fraction. AE doesn't display the affected layers in the viewer until the next whole frame.
The precomp these layers in is ahead (in the main comp) by the same fraction these layers are behind. Additionally, some time after I precomped I noticed AE had changed the start timecode for the comp to -0;00;00;01. I thought that was weird and changed it back to 0. Maybe that has something to do that.
I can't find a way to slide the layers back to where I want to start -- maybe AE is trying to protect from sync issues? But I'd like to get everything back onto real frames so I don't mess up my editing. I have an earlier version that doesn't have this problem, but I'd lose a good bit of work going back to it.
Are you sure that every comp is the same framerate of 29.97? Maybe something in there is 23.976, or 25, etc.
You can put the current time indicator on the frame where you want the layers to be begin, select the layers that have shifted fractionally, and press the open-square-bracket key ('[') to align them in time again.