Leave the Nvidia controls at default. Use the monitor controls to change the brightness/contrast/RGB or whatever Spyder3 tells you. Having 2 layers of software, Nvidia and Spyder just allows for more things to go wrong, imo. Maybe I am wrong about this...
This is what bugs me about the Spyder and probably other calibrators. It requires changing the physical settings of the monitor. Makes it impossible to have more than 1 profile.. for example a daytime one, when it's brighter in my room and sunlight, and evening profile when it darker and using artificial lighting.
I think the first time someone calibrates a monitor, the first reaction is... it's too warm..... it's likely, I have no way of knowing, that your monitor color is fine.
Monitors are inevitably shipped too bright and the colors are too "cool".
btw. I don't run Vista but, I hear, there are quite a few people that have had profile problems being reset, depending what application is being run. You might want to do a Google/whatever search.