Ari,
Do you have the Kensington Mouseworks beta2 installed? I recently learned that it was the cause of my own application priviledges woes. They have beta3 now, and it solved the problem for me. No more root.
CQO
I had a problem with placing new apps into the main application folder. I was told I did not have the proper access. But today I learned that Kensington's Mouseworks (beta2) created this problem. The new release (beta3) appears to have fixed the problem. You still have to do a manual uninstall...