Plugins not saving in Vista
Every time I open pcsx2 it says it needs to be configured after I already have. I'll configure something specific, like the controller plugin, I hit ok, and if I go back to configure it again, every thing is cleared. Its the same with the other plugins.

I was wondering if it may be some sort of Vista permissions problem, I've noticed before Vista does not always let applications save information in the program files folder, maybe this is the same?

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disable uac or run pcsx2 with "right click->run as admin"
CPU Core [email protected] | GPU Nvidia Geforce GTX 570 | RAM 8GB DDR-3 1600MHz CL9 | OS Win7 Ultimate (x64) SP1
EMU PCSX2 v1.1.0 r5645 | GS GSdx SSE4 r5632 | SPU2 SPU2-X r5559 | PAD LilyPad r5403 | CDVD cdvdGigaherz r5403
Have you tried "right click > wun as administrator" or moving PCSX2 folder to a folder with permissions like the "Documents" folder?
Core i5 3570k -- Geforce GTX 670  --  Windows 7 x64
I had the same problem the solution is to give your the pcsx administrative access.

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