I have been using after effects for about 5 years now and I never had this problem. I am using After Effects CS6 on Windows 7 3.2ghz I7 6 core with 32gb ram.
The problem I have is as I am completing the first draft of my rotoscoping and I play back, my masks don't follow EVEN though the squiggly lines are stuck pretty good to my character. It is as if the roto masks are stuck while the footage is still playing in the background. The whole sequence is 20 frames and the majority of the frames work fine. Somewhere in the middle it glitches or so and messes up every other frame. I tried restarting the program as well as my computer. Unfortunately I don't have a second computer to verify if the problem is in just my machine. I was hoping someone can help :( I have attached two images, one of a proper roto and the second is the messed up roto I am having a problem with.
The 2 layers are exactly the same just different names. Normally I would do my roto in Nuke for my classes at school but I was not able to get an official copy for my home pc, so I am stuck with After Effects until school is back in session. I love after effects, just not for roto >-)