is your application UAC-aware? This problem has absolutely nothing to do with the installer. It's your own application that seems to have an (UAC) issue. Perhaps you are trying to write to protected Windows resources from your own application? For example, do you try to write to HKEY_LOCAL_MACHINE from your own asInvoker manifested application?

And why do you have to run the installer "as administrator"? The per-machine installer always runs elevated by default. Using "Run As Administrator" has absolutely no effect on "requireAdministrator" manifested apps.

BTW, here is a very brief description on how to make your app UAC-aware: