I've been experiencing the same issue. I upgraded to 10.6.4 and I lost several fonts. The interesting thing is I also lost several power point images I had created. Shapes and lines were missing even though they did not involve the offending fonts, at least not directly. There was text elsewhere in the image that used it. Why this should obliterate the rest of the images I don't know.
The three offending Fonts for me were:
1) Times New Roman
2) Arial
3) Brush Script MT
Anywho, I managed to fix this on my machine so I'm posting how I did it here. I'm not so sure as to the why, but here it goes.
On my machine I have 4 font folders
1) -> System -> Library -> Fonts
2) -> Library -> Fonts
3) -> Users -> Me -> Library -> Fonts
4) -> Applications -> Office X -> Office -> Fonts (yes, I'm still running Office X from 2000)
Inside of the Font Book application, it was kind enough to point out I had duplicate fonts. Some of these were the fonts in question and others caused me no troubles. Go figure. Anyway, disabling one or the other of the duplicate fonts did not fix the problem.
Here's what did, though. In my case the duplicate fonts existed in the second of the font directories above (henceforth referred to as Font2) and the third of the font directories listed above (Font3). I browsed to these directories and copied the fonts to my desktop to have a back up. Back in Font Book, I told it to remove each instance of the Arial and Times New Roman fonts that would not display correctly in Excel (for the moment, I left Brush Script MT alone, kind of like a control)
Now at this point there were no Arial or Times New Roman fonts in my Font Book. Turns out they were removed from Font1, Font2 and Font3, so good thing I have a backup.
1) Opened up Excel. It did its font menu optimization thing and sure enough, I couldn't see anything.
2) I close Excel.
3) I double clicked on Times New Roman that I had in Font4. Font Book opened it and I chose to install it. It put it in my Font3 directory.
4) I opened up Excel. It did its font menu optimization thing. Suddenly I can see Times New Roman again!
5) I close Excel.
6) I double click on the Arial Font from my Font4 directory. Font Book opens it and I install it to my Font3 directory.
7) I open Excel, it does its font menu optimization thing and suddenly I can see Arial!
8) I close Excel.
Now at this point I'm wondering if my old font files got corrupted and because I was installing using the ones from my Font4 directory (which avoids the system directly) I was getting them back. So to test, I told Font Book to remove Times New Roman again, I go through the test of opening and confirming in Excel, and then I install the Times New Roman font from my desktop that I had copied out of the Font2 directory. Everything works fine in Excel. So it's not the file that was bad.
I was also wondering if I needed to remove all instances of the fonts or if just one was causing the trouble. So I go back to Font Book and remove the instance of Brush Script MT that was in my Font3 directory. When I opened Excel I still couldn't see anything.
I reinstalled the copy of Brush Script MT from the desktop and tried removing the other instance of the font, the one from the Font2 Directory. Excel still shows nothing. I then reinstall the associated font file from the desktop. Excel still doesn't like me.
Finally, I removed all instances of Brush Script MT and installed at random one of them from the desktop. Suddenly Excel likes it.
So I don't know what the problem was, maybe an associated was bad, but either way the only way I could get my fonts back was to remove all instances of the bad fonts from Font Book and then install the font again.
In between removing and installing I would go into Excel where it would refresh its Font list at startup. Not sure if this had anything to do with it either.
All my fonts now display correctly and all my powerpoint drawn images show up as well. I hope this helps someone else!
-Kevin