The whole Windows / user permissions / Administrator rights thing is a bit of a confusing mess. For example, I was told by Sonic Core that I need to run the audio card software as Administrator, so I did so and Windows would always ask, "Do you wish to allow this program to change your computer blah" and I'd say yes (of course) and all was well. Then I ran it as myself and all was still well. Now when I run it as Administrator, Windows doesn't even ask me "Do you wish to allow this program to change your computer blah" any more. Along similarly confusing lines, it used to be that switching between myself and Administrator when running X2 caused X2 to do its "Personalising your user settings blah" thing every time. Now I can run it as either and it no longer does this.
So, in summary, I'm going to make a coffee...
*glug*
I think what's happening here is that as you're not logging out and back in again as Administrator, the application is running as yourself as Administrator because doubtless you have Administrator rights which is why there's a difference, or no difference, or bananas, between running an application as yourself who has Administrator rights and running it as Administrator as yourself who has the Administrator rights.
*glug*
Bananas!