Windows Vista contains a nice utility called Program Compatibility Assistant which tracks the applications which might have problems with running in Vista. When you start an application which is detected to have problems with Vista you will be presented with a box like the one below, and the necessary compatiblity settings are automatically applied. In some cases the Program Compatibility Assistant solution to a compatibility problem is to set it to run as in Windows XP with Service Pack 2. What the Program Compatibility Assistant do in my example case is to determine that an application need to start with elevated privileges when using User Account Control. Of course this is a problem when the user running the application is just a standard user as he or she cannot start and use the application.
Regardless of what the Program Compatibility Assistant do the compatibility settings are stored per user and application in the registry. Have a look at this registry key to manually remove or just to have a look at what compatibility settings have been applied on your computer: HKEY_CURRENT_USER\Software\Microsoft\Windows NT\CurrentVersion\AppCompatFlags\Layers.
The solution to resolve the problem with running certain applications elevated can in many cases is resolved by turning off User Account Control as a last way out, if you have not already disabled it.