I'm sorry to hear that.
For the scanner service needing to be started manually,the service may be taking too long to start with Windows startup and perhaps failing,and it remains off because it is set to Take No Action under the recovery section,and I believe that is by default(I don't remember changing anything with that service,at any rate.)
You could increase the time-out further in the registry if you would like to,that may give it time to start,following the registry editing instructions above.
Or you could set the service to try again after it's first failure.If you prefer to do it that way,click the start orb,type in Services,click it,scroll down to Spybot-S&D 2 Scanner Service and doubleclick it,go to the Recovery tab,and under First Failure,select Restart the Service,then click Apply and OK.The service may start Automatically after logging into windows if it tries again on it's first failure,or it may not if it still runs into the time-out again,it's hard to say,but it's worth a try,if you like.
Is Spybot the only antivirus on your computer,or do you have any others?