I've had some Vista issues as well. Surprisingly turning off aero makes the emulator run slower!
That's right, I turned off aero(not fully because currently microsoft hasn't provided a way to fully turn off aero) and the emulator ran slower.
Anyways, PJ64 said that they'll be developing for Vista pretty soon. Give them another 3 months and we'll have a version addressing Vista and with that, I think our bug issues will be mostly resolved.