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Is there any settings i could use to remove FMV stutter? i mean. currently using Hardware mode for games to scale it up and the only thing i could for the stutters is to either change it to software mode or closing and resuming the windows (albeit with chances of CTDs) Thanks!

GIF is attached to show what i meant.
sorry for the low quality though. too big.

and oh! currently using the Latest SVN builds

[attachment=48886]

[attachment=48887]

What games are you trying to play exactly?
Try changing the interlaceing settings in Gsdx a bit and see if it helps. If you are using speedhacks (EE/VU slider) try turning them off as they can also cause flickering FMV sometimes.

Are you playing from an ISO or directly from he disc?

If videos flicker like that, just press F9 and it will be fine.

There is also a gamefix in the Emulator Settings->Game Fixes called "Switch GSDX to Software Mode during FMV's" to automatically do this then switch back to Hardware Mode again once the FMV has ended.