How can I prevent Windows from disabling Aero when I use my secondary monitor?

I'm guessing you almost always have a browser open, like a lot of folks I know. I've seen this problem in both Internet Explorer and Firefox when running a browser on a display attached to a secondary GPU. The fix for that is to disable hardware acceleration in the browser - it doesn't always play nicely with DWM for some reason. (I seriously doubt you'll see any performance hit as a result of this).

It's possible there are other things going on, but some idea of what's ALWAYS running would be helpful to pin it down.

There's a problem with Displayport in combination with Aero. Try Windows Aero without the displayport (DVI > Displayport adapter should do the trick). That did work for me at least.