The exact same thing has happened to me. BtS worked fine for months, then about 6 weeks ago the entire interface disappeared during gameplay, and while hitting ESC still brings up the menu, clicking on Options results in absolutely nothing happening. In addition, when the game loads, it completely skips all of the opening movies and goes straight to the main menu (not that that's a problem, but it may help someone figure out what's going on), and I can't access Options from there either.
I've uninstalled and reinstalled numerous times and tried with and without the 3.17 patch and the BUG mod (the only mod I use), but it's the exact same problem regardless. Vanilla Civ IV and Warlords (Gold Edition) still work perfectly, but it sucks playing those when you're used to BtS. Help?