Running a registry clean using tune-up on a Windows 2008 server detected Missing fonts. Selecting to clean up the missing entries caused all the fonts to display as wingdings or other characters, making the system unuseable.
We had a similar issue with a different registry cleaner on a Windows 2003 server recently also.
I re-enstated the fonts from backup, but each time tune-up was run it still detected the fonts as missing. Thinking some were corrupted I also copied and installed the fonts from another system, but tune-up still detected them as missing even though they work fine.
Here is an example of one of the errors detected.
Missing font Levenim MT (TrueType)
The registry contains an entry for the font “Levenim MT (TrueType)” under “HKEY_LOCAL_MACHINE\Software\Microsoft\Windows NT\CurrentVersion\Fonts” that points to the missing file “lvnm_4.ttf”.