Ok what you are describing is indicative of having a small utility program on your Mac along the lines of HideAlways, Shoo Apps, or another one I can't remember right now

o) which do two things:
-they make the inactive app's icons translucent (which against your dark desktop makes them appear to darken)
and
-they hide the windows of inactive apps
Take a look at your "Login Items" tab in your System Preferences Accounts pane to see if either of those programs are installed and loading at startup first.
The icon "dimming" as they call it in some utilities can also be instituted or disabled in some general utilities packages (MacPilot and Onyx for example). Mac Pilot also has a setting to enable/disable what they call "Single Application mode" that hides all background windows.
Your problem is indicative of why I love Macs- the behavior is driving you crazy, but I would not live without it! Having dimmed background windows all over the place from inactive apps just does not cut it for me, but I can modify that behavior very simply! Maybe Spaces could take care of my needs, but Shoo Apps does fine for me!
So anyway, start off with the info above and maybe that will get you back to the stock way that the Mac handles inactive apps anyway! Good luck!