This is a bit strange!
I have a site that I've upgraded from ATA 3.7.3 to 3.7.10. (WP 3.5.1) It's been running just fine for years before and after upgrading... No problems!
I was doing a pagespeed test and noticed that the css and js were not in an external file. So I went to the ATA "Configure CSS and JS" settings page and changed to "External" and saved. Upon refreshing the front page... All css and formatting went away. I went back to Inline and all's fine again.
I combed through the BFP archives and found this thread...
and tried the "Remove bfa_ata4 from the database" but that made no difference.
Any clue as to why selecting External files breaks the site? I have had no problems on other sites...
I'm scratching my head!