This is just to update for other users who might have this problem down the road. I had a chat with Richard and for this case, the best way is to use AE because pixel accurate positioning is needed. My problem lie in the refresh rate of the Fusion Mapper. In the Catalyst frame rate settings, I was using 25fps. Turns out I needed to use Screen 2 div 3, which for my display is 25.01Hz. Turns out that that 0.1 Hz was causing my inconsistent glitching. It started doing it again when I turned off full screen mode on Screen 1, so if anyone else runs into this problem, keep both screens in full screen mode.

Cheers,

Kevin