Administrator ideas

I recently had some annoying spyware i had to get rid of on my Windows 7 operating system (don't worry its gone now) and i noticed that some of the newer spyware had a little trick where it disables a lot of Windows actions. Regedit, folder options, and system restore all turned off. They claimed i wasn't the administrator even though i was logged in as the administrator.

I managed to get regedit permission again by running another program after the spyware was gone. When i ran spybot, it played right into the whole spyware scheme and said i wasnt the administrator and couldn't turn on system restore because of that reason.

At the time, i didn't even think of right clicking the program and selecting "running as administrator" (btw, why doesn't it mention trying that in the error message you get?), instead i went into the registry and changed the one "System Restore Disabled" registry key back from "1" to "0" and bam i could do System Restore again.

Shouldn't spybot be able to know the difference between someone logged in as a regular user and admin user that had a few registry keys changed by some spyware? I mean it still said Administrator in my user account description and everything.