Just to add - if you have your UAC settings set to "Never Notify" (the least secure setting) then Windows will simply refuse the action that throws the UAC notification. I'll bet that's what's happening. You can prove this by running the second instance as administrator.
I'll add that since this is an unsupported method, I have no idea what kind of things it can screw up. I have always been careful not to open the same profile in each instance, for example, for fear that it would corrupt the profile. Likewise, I never select the same equipment in each instance.
Tim