John- You might try looking in Help>About . . . for system hints, and then try fixme.bat again. Then try installing a different printer driver and switching. Don't forget to look in UFT Help and Pd.ini.
Then give up and do a careful re-install of UFT 3.0 and the 3.1 upgrade.
I don't recall any users reporting Font Indexing problems with UFT 3.0, but I have personal experience with screwing up the Print and Font Setup indexing while playing around like this in UFT 2.x. Good luck, john