Could you please explain further?I want to be sure to give directions to get Spybot to run once on reboot the way that you want it to.

From reading your post,I'd guess you might have been trying to get Spybot to run once at reboot,but instead of scanning or fixing,it's just been opening the program,is that correct?
You can get Spybot to run once at System Startup.To do so:
Go into Spybot > Mode > Advanced mode > Settings > Settings > look for "System start" (located half way down the page).
Check the option: "Run program once at next system startup".
Along with that,there are also some other options you can select,including
Run check on program start,which should get Spybot to run a scan.
And also,Fix all problems on program start.
This attachment shows some of the options to look for:
http://forums.spybot.info/attachment.php?attachmentid=2729&d=1229137085