Installing Star Trek Armada 2 on Windows 7?

Wow! Haven't heard of this game in a while. If you're going to play it though, grab Fleet Operations as it brings the game up to modern standards (in graphics and gameplay). It will require your disk but it has a custom installer that works (last i checked anyway) on windows 7.

If you're sure that you want to play the game stock, open the CD manually in explorer, then go to the Setup folder and launch Setup.exe with administrator rights (i suspect you may have been launching the autorun program as administrator instead).