Having this exact problem too.
Consider updating your OSX to 10.10.4
Apple fixed some big bugs that affected After Effects in the 10.10.4 update.
I should update this thread.
I updated to the latest OS, while it hasn't completely fixed the problem, it's far less frequent.
I've been having a similar issue. For me, it has more to do with the undo function.
For instance, when I would undo a change of position for a shape layer, the timeline would show the undo and in the composition viewer the boundary box would also reflect the undo, but the actual shape image would remain in the same position. I haven't found a way to get the image to realign itself with its boundary. If after the failed undo I would change the position, and the shape and its boundary would both change but now in two separate positions.
This issue is also intermittent but requires a restart of the program.