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I'm running the FF X cutscene gamefix w/ no speed hacks. I've tried going to native resolution in GSDX but that hasn't fixed the problem eiether. I'm using the 0.97 PCSX2 beta and playing the NTSC version of FF X.

Whenever a prerendered cutscene plays, the scene right before it begins to flicker on and off over the prerendered cutscene as it plays; which is really distracting. I'm not sure what's the problem and I haven't heard of anyone else having similar problems.

Try suspending (ESC) and resuming the emulation again. That did the trick for me (sometimes). Another way would be to use software renderer with F9. But afaik this issue is fixed with DX10 mode of GSDX. Since I have Win7 this problem did not occur, only on Win XP with GSDX 9.