spyware scanners only get 50% - 70% of all known spyware. Using two scanners help, but that's a large percentage of spyware that still get by. I just scanned a system with Microsoft's Antispyware and it removed every thing it found, but the realtime protection was still indicating that something was trying to change my browser addresses.
I want to put together a guide to tracking down that last 10% of spyware that gets overlooked by the scanners. Some simple developer tools can be very powerful in the tracking down spyware. Sysinternals has a good collection of tools that I want to talk about with tracking down spyware in mind.