Poor Visual Studio 2005, aka Whidbey. Developed and released before Vista, it's Vista-blind. Say you're building a COM component and one of your build steps registers it, writing to something under HKLM. Unless that instance of Visual Studio is running elevated (perhaps because you right-clicked and chose Run As Administrator) the registration will fail. The fix: close Visual Studio, run it again elevated, repeat your build. It's a little frustrating.
Every month that goes by is going to make this better. Eric Appel has a nice summary of what you can do now: install a pair of updates (one released, one in beta) and set Visual Studio to always run elevated. You'll need to consent every time you run it, so I actually skip this, run non-elevated most of the time, and when something fails I close and re-open Visual Studio. If you would find that super frustrating, go ahead and mark it to require Administrator. It's also a good habit to test by double-clicking your EXE in Windows Explorer rather than hitting F5, so that your app is elevated or not elevated according to its own manifest and not according to the way you started Visual Studio.
It's a transition time. It won't last forever.