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I remember playing this game on my old PC (prescott 3.2GHz) and getting close to 60 fps most of the time.

I decided to try the game out again on my current PC (E8500 3.2GHz) only to find I get slowdowns (drops to 50fps). It is very playable, but I expected less slowdowns not more.
I'm running this on the 0.9.8 version of pcsx2 available from the homepage. I can't remember what version I ran it on before (or what plugin version I used).

I tried the game with speedhacks, none of them has any effect on the fps at all. The VU cycle steal @ 3 seem to boost my fps to a constant 60, but you can still see the same slowdown in game.

EE is usually at ~80%, while GS is always 50% or under. I tried the game on 3x native or 1280x1280 custom (which was the setting I played on with my old PC), neither changed the fps at all.
Running at 2x native boosted the fps by about 2-3 (still doesn't allow constant 60) but looks worse than when I ran it on my old pc.

Any idea what version of pcsx2/gsdx would run FF12 better? or is there something I'm missing in the settings?

Hmm are you by any chance running it off your DVD disc? If so try making an iso image of it using imgburn and running that.

I'm running off iso.

I also noticed graphical anomalies that weren't present last time I played it (mainly loss of transparency effect in some places. Most noticeably when you enter a new area and the area name shows up, a large chunk of the screen ends up white).

I've turned off all speedhacks and am running everything on default.

What version of pcsx2/gsdx is best for FF12?

EDIT: Sorry for the double post.

Try the 0.9.7. The 0.9.8 might be slower than 0.9.7 for some games.