Drupal keeps loosing track of my Zen theme?

Hi this is my first Drupal project and I'm not sure if this is a Zen problem or some other kind of problem. I am just about to announce a new site (iap.csail.mit.edu) and all of the sudden Drupal seems to have started loosing track of the Zen subdirectory where I have my sub-theme stored. It happened once on a day where I don't think I touched the site at all and I've had it happen for as little as going into adminster and clicking on themes.

(iap-dev.csail.mit.edu is broken in this manner at the moment so you can see what the broken behavior looks like there)

I've tried deactivating and re-activating the theme and copying the theme into a new subdirectory. The only way I've gotten it to work again is by copying the files for the fixed with theme into a new subdirectory..activating THAT as a new theme an then applying my graphics, overides.css, page.template.php etc to the directory as if I were building the theme from scratch.

The site is just about to launch, we are already past our deadline, and I am concerned! If anyone has any ideas they would be greatly appreciated..

Thanks!
Jordana