There are some patches that Microsoft has offered for SLI in vista that you can't download from windows update. You said that you have all updates; do you have SP1 installed? I'm pretty sure the SP includes the SLI updates. If you do, then I'm not sure what your issue is. I have the same OS (with SP1), and SLI runs just fine for me.
The one problem though, is that SLI does not always return an increase in FPS, and can actually decrease performance. The only reason I suggest this is because you apparently dual boot, maybe the games that you are running in vista don't actually benefit from SLI (which can happen even if they have SLI enabled in their profiles).
I hope my suggestion for grab SP1 helps, but if you already have it, I'm sorry that I can't assist you. Good luck!