JJM
Is Vista your OS?. In my experience and that of some other users I encountered on some computer boards Spybot does not play with Vista as well as it played with XP. After some experience on my Vista PC I uninstalled it because of problems similar to yours.
Whether Spybot is the best antispyware or not is also debatable.
I don't think that the point here is whether Spybot is the best available, it probably isn't. It's a very good, valuable tool, it's free, and it's a decent anti-spyware agent, plus startup manager.
As to whether it plays well with Vista, to the best of my knowledge, it may not be designed so. Many other older XP programs won't either. Heck, for a while there, Vista wasn't playing well with Vista. Many of us still happily run XP with very little desire to change.
It's just fortunate for us that people take the time and effort to invest their talent into programs that help us, and do it for nothing.
Spybot's "Tea Timer" can be unmanageable if it's not installed after or with a clean install of Windows. It seems to want to revert the registry, scan files, and does make a miriad of announcements, but after a while it appears to calm down. Now that it's new version has been on my computer for a while, every announcement relates to something I've done, and I'm good with that.
Now, "Ad Aware 2008" doesn't impress me as much as the earlier version. I've reinstalled it a couple of times after an update crash, and an application failed to start debacle. It also seems to take twice as long to scan the same machine which now has less programs installed.