yeah, I tried the whole modifying the master slide thing but the missing fonts aren't on there, they would have come from slides I deleted as well or already replaced the fonts on so not sure why they are lingering....
oh wait...I think I might have just figured out something. The whole "revert to previous version" wouldn't that have something to do with still remembering fonts used in a previous version? I'm going to try and see if I can duplicate the current document in some way that makes it a new version with no history in it.
Other than that I was going to try exporting to '09 do the replace fonts tool that was in there and then open it back up but I'll have to modify the transitions and shadows that were new to current version of keynote.