I would recommend using the latest SuRun 126.96.36.199 Beta http://forum.kay-bruns.de/post/4076
The System Menu is the one you get by pressing <alt>+<space>.
I guess you mean the "SuRun: Run As Administrator" entry in the context menu when right clicking apps.
Balloon tips should not pop up when turned off.
I'll check this out this evening.