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I suppose i will list what I have first since it may be related

OS: Windows 7
CPU/GPU
E2200 Pentium Dual Core CPU OC 3.0ghz
NVIDIA GeForce 8600 GTS
Sound Blaster Audigy SE

My problem is the option in GSdx plugin to enable more than 1 core is grayed out. The option is called SW Render Threads. It is grayed out and only has 1 in the box.
I seem to be getting not so good frame rates they are around 45fps and the sound and video are a bit choppy.
Not sure why?
The version is 0.1.14

It only shows if you have selected software mode and the vast majority of time software will be slower then hardware.

What should my configuration be to get a acceptable framerate that isn't falling to 80% causing the sound to stutter then? I'm trying to play .hack//GU on my PC because I don't want to move the Playstation 2 from room to room ;o And I have a nicer screen on my PC

Not sure though I was able to fun .hack Infectipn the other day at full speed before it crashed and I got annoyed and didn't decide to check if it was a bug at that point or a random crash. Are you on the latest beta?

I believe so
Beta 1329

Well then play with the speedhacks I guess. Also if you have a high D3D res back it down a little as that could be your issue.