For starters, Spybot alone is not even close to enough. Unlike AV programs, malware removers need to be run in great numbers. As many reliable free ones as you can find. You also need to make sure System Restore is switched off, or quite a few little buggers will just come back after you reboot.
If you run Adaware, AVG Anti-Spyware, and Windows Defender, my guess is that you'll come across a large number of things Spybot missed. Sadly, no one anti-spyware program will catch everything.
Recently I have run into a problem that I have never seen before. It started spontaneously. I did not download or install new programs. I'm sure I picked up something malicious from a website, but nothing intentional.
That being said, when I am using IE or Firefox a window in IE will spontaneously launch and attempt to load a webpage. These webpages range from ***** singles to some sort of Yahoo page. These launches are spontaneous and I have not found a relationship between what I am doing on the computer and what launches in IE. I do have to have one browser or the other open.
I have run Spybot Search and Destroy and my virus scan. Both did pick up some problems. I "healed" or removed the files, but the spontaneous launch still occurs. I have reinstalled Firefox and rolled by IE updates to no avail.
I am using the latest editions of both IE and Firefox on a Windows XP machine with all the latest updates. If you think hardware is an issue I can provide that information later, but this definitely seems like a software/malware/adware problem.