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Strange thing is that everything used to run fine months ago. I have also tried the old versions of the emulator and plugins and even the versions which used to run without these slowdowns.
So it seems that some configurations of the graphicscard could be wrong although I'm sure that everything is set to maximum performance or maybe it is because of vista service pack 1 using to much of RAM. The new nvidia driver could also be a reason.
I have no idea, exactly..

Issue solved!
Tried the suggested plugin of "gsdx 0.1.7" and it solved the slowdown problem. Make sure that u use direct x 9 as direct x 10 will cause a slowdown when the fight menus during battles appear on the screen!

So everyone with a similar rig as mine should use that plugin with direct x 9 to play FFX with less annoying slowdowns.