Snadds, is your version of Spybot running with the scan priority option set to "time critical"?
You can check this by going into spybot advanced mode, click on the settings tab on the left, from the list shown there's another option labled settings, click on this, then scroll down to the scan priority option.
If it's set at time critical, this can cause system instability.
I have mine set at "Highest" and while the scans running it seems it's not doing anything because the scan status bar at the bottom doesn't do anything until the scans completed. Because it's set at highest the scan is taking priority over other processes and so the scan progress doesn't get shown.
Hope this helps, dagwoood.