I really don't see much wrong with your setup save the fact that your computer won't shutdown -- you've just misunderstood some of the processes and though them to be malicious -- we all do it.

But the shutdown thing is a nuisance. Try getting the latest versions of your drivers; some buggy ones can refuse to unload and therefore lock up your system on shutdown. Also modifying your boot screens can do this too, though I'm sure you would've mentioned it if you had

http://www.annoyances.org/exec/show/article07-016

There