I seem to have spoken too soon. The very next document I prepared
had the same boxes-rather-than-letters problem.
That said, I cleared the font caches again and, after restarting,
the document looked correct. Perhaps this is a coincidence. Or
perhaps there is something amiss with the way my computers are
caching fonts. Sigh.
Well, if your engine is pdftex (from an unpatched TeXLive 2008) then
chances are you're running into the nasty (TM) font cache bug:
http://www.tug.org/mactex/fontcache/
Oliver
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