Whenever your UAC prompt appears and asks for your permission, you may have noticed that it darkens the screen and temporarily turns off the Aero interface – and it itself appears without the transparency. This happens in Windows Vista, Windows 7 and Windows 8 too. This is called Secure Desktop.
When you use Flip 3D in Windows Vista, however, you can see it as having the Aero transparency. You can see it below in the first image right in the front. Here the UAC prompt appears with the transparency.
This is actually a security feature. Using Secure Desktop prevents other applications from manipulating the UAC prompt. When you carry out any task which is in need for UAC permission, for security reasons, when Windows asks for the UAC confirmation, it separates the UAC prompt dialog box from your running desktop process. The UAC dialog box runs under a secure mode desktop, so that any malware which may be running under the regular Aero enabled desktop, will just not be able to access the UAC to authorize any action.
Nevertheless, if you would like to stop blackening out of the screen when the UAC prompt appears or are simply a Aero lover who likes to see the UAC prompt with the transparency, you can disable Secure Desktop. Do note however, that by doing so, you would be opening your computer to possible security risks & threats, and hence is not advisable.