Hey, SpybotSD might turn up a piece of spyware, who knows.
It really is as easy to work with a program in the Windows environment as it is with Msconfig.
Reinstalling the OS is the easy way out for a savvy user, with backups available, even a clean drive image.
You would have to do a complete reinstall of your programs. But as you rightly pointed out, you could screw around for hours otherwise and not solve your problems.
I have a goofy registry problem in my Emachine T-5026, where I can't use the Windows firewall because I removed "Macafee Security Center" (which didn't do squat but nag you to buy more Macafee garbage. The Norton AV and apparently any other security program was routed through the "Security Center" nonsense. But, my OS is tied to a restore disc and a reinstall would just reinsert the suppository so to speak.