Hello: this is a problem I am having only with the production site, not my local. My local uses MAMP and multisite install.
For a while everything was fine. Then suddenly some (but not all!) pages are throwing massive ugly "user warning: Duplicate entry 'themes/garland/minnelli/minnelli.info' for key 'PRIMARY' etc." warnings. I mean, 10 inches of the stuff. Obviously something wrong with the theme.
So I go back to my /admin/build/themes/select Site Building => Themes => List page and find that my subtheme is no longer enabled. So I enable and select my subtheme and make it default.
Works for a while and then, boom, this happens again and the sub-theme is no longer enabled.