Sorry I've disappeared so long. I found what I've called a "semi solution" to this problem. It's still not ideal, but it works. I've blogged about it here: http://nerd.steveferson.com/2011/01/18/solved-cc-tiberian-sun-on-windows-7/
Anyway, I too found that when I went back to Windows (Windows Key) and back into the game the menu was there. It's not "frozen" as such. You can still select things, you just can't see what you're selecting.
At first I pressed the windows key every time I clicked to change a setting, so that the menu would be "redrawn" in the new state. However this wasn't entirely satisfactory.
Luckily I soon discovered that the menu would appear if I scrolled. I was using a laptop so I scrolled by running my finger down the right hand side of the trackpad (from top to bottom) while the cursor was over part of where the menu should be. I'm not certain, but I imagine the scoll wheel on a mouse would do the same.
It's not really a fix as such, but hope this helps.