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Don't know about anyone else but these two options are slowing down the emulator.

I've tested okami, KHII, KH:chains of memories and rogue galaxy (really helped)

all increased in speed from disabling both these options, sometimes dramatically.

my specs;
i5 460m 2.5ghz
4gb DDR3ram
ati 5650m 1gb DDR3

PCSX2 0.9.9 r4962

anyone else find this?

might happen.

If Rogue Galaxy gets slower from the mtVU hack, you have some misconfiguration.
This game is known to largely benefit from it.

I tried it on shadows of the colossus and god hand as well and they were the opposite.

Thats weird with rogue galaxy, it definitely sped it up for me I would do laps round the city and the difference was noticeable.

maybe its like VU cycle stealing; Okami suffers really bad slowdown with this on three where rogue galaxy speeds up, might just depend on the game?

Yes it does, and you should never benchmark by running around and checking how it feels.
Use the FPS meter in the window title or better yet, a tool like fraps