drragostea:
You can schedule Spybot to start, update, scan and then close at anytime. There is no restriction that you can only do that when you reboot the system.
grinnz:
In your desire to automate the entire process do you check the results of the scan that are preformed; i.e. Checks.yymmdd-hhmm.txt or Fixes.yymmdd-hhmm.txt files?