The admin level warning is a Windows function that's designed mostly for Vista I guess, where even admins need to make sure they run apps elevated if they want admin rights. So the text was written with that in mind, I'll take another look at it in this context.
Basing the warning on the number of open immunizations sounds like a good idea as well. I logged that as a feature request here:
Immunization: warn about missing admin rights only if unimmunized
Which Windows are you using? Spybot-S&D starts in the profiles folder and looks for all user folders in there, loading their registry hives and locating specific paths from those, so that even changed appdata paths shouldn't hinder it. Maybe you could also use regedit while Spybot-S&D is running to see if other users registry hives are actually mounted.