I would just add to the above that I have noticed for example that vector paint can easily add to the file size of the AE project (alot in my experience and also slow down saves 😛 ), as you may find that your painting many strokes to accomplish a task, im not sure if it is the same with the paint effect but im guessing so but this involves storing alot of data.
Just a thought as to why there might be such a large difference between your different projects.
Regard
Chris