While I have not used Vista, I would presume when you right click on your shortcut and choose properties, there is still a compatability tab. use that to set the compatability mode to either windowsXP or windows98 (98 preferably if available). Also make sure your power usage mode is set to always on. Since you said you have a Turion x2, use
http://www.amd.com/us-en/assets/cont...onitor_120.zip to set your power state. EQ seems to NOT wake a CPU up into it's higher power state which is what you force on by setting the power scheme to "always on". Make sure once you get done you turn it back to "Portable/laptop" or your battery will die way quicker that it would typically.
Also, unless you copied your EQ folder so you have 2 seperate folders and run the eqgame.exe out of each folder, you CANNOT set affinity to 0 on "one instance" then set the other to 1 when it's the same program from the same folder. What you will end up with is the program either going all crazy and potentially causing file corruption due to CPU cacheing to both cores yet not being synced with eachother or it will simply run on the last core you set it to. My money is on data corruption is what caused your major issues after messing with CPU affinities the first time.