I wanted to point out that on further use I've ran into similar issues. Nearly any game with a complex intro fails loop detection, or detects the loop improperly. Most fighters fail as they have complex intros and several transitions (attract mode, demo mode, highscore mode ect).
Is it my understanding that you are doing a simple getpixel point check then? Imho this isn't gonna work well at all. Disable compression (as others have suggested) and do crc checks of the spit out image files. Only when the frame is exactly, exactly, exactly the same will the crc check pass. You'll have to do a get pixel test on top of that to get the color level (make sure it isn't matching on an all black or all white screen). Of course, depending upon how accurate the render method is, that may cause even worse performance, I dunno.