Hi John,
Since TextEdit and other apps can use the fonts, then there's nothing wrong with the fonts themselves, as you've already noted.
Fontnuke clears font cache files, but not necessarily all of them. Not as likely, but Font Book may be causing some of the problem. To reset Font Book, follow the steps in
Undoing Font Book. Note that you will lose any font collections you have created. Doing this will also clear the font cache files for your user account. This also resets Font Book's database. Any fonts in the /Library/Fonts/ folder, or the the Fonts folder of your user account will now all be active.
With a clean database for Font Book and caches once again cleared, things may now work as they should. If not, continue on.
MS Office keeps its own cache files, which if corrupted, may be keeping Arial and other active fonts from appearing. Close all Office applications and remove the following files. The tilde (~) indicates your home account.
~/Library/Caches/com.microsoft.browserfont.cache
~/Library/Preferences/Microsoft/Office Font Cache (11)
For Office 2008, the latter is:
~/Library/Preferences/Microsoft/Office 2008/Office Font Cache (12)
Next is Quark. It also keeps its own font cache files. Close Quark if its running. For version 6, go to the /Applications/QuarkXPress 6.0/jaws/ folder and empty it out. For version 7 and 8, I believe the jaws folder has been moved to the Quark folder within the Preferences folder of your user account.