Strange Font Problems

I have a user who is running a Mac G5 with OSX 10.4.11.  We've tried resetting the system font to correct an error in Mac Mail, and Safari, IE, and Mozilla where the default font in these applications was Alien League.  Now everytime the user shuts down and restarts Mac Mail there is a different font being used.  Sometimes it will remove just the first letter of a word, and sometimes a line of text will be condensed down to overlap the same area making it un-readable.  The problem has spread to other applications such as Acrobat, Illustrator and InDesign where the file menus open but there is nothing contained in them, it's just empty space.  Has anyone come accross this before?  Could it be a virus?  Could the system fonts be corrupt?
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Here is some general information about fonts.

The first thing I would do is to open the Accounts system prefs file and create a new user. Log in as the new user and see if you still have the problem. If you don't one solution would be delete the old user. On the other hand you could trash the fonts that are specific to the problematical user.

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sharkbot221984Author Commented:
Thanks strung.  I ran the disk utitlity -> repair permissions, and restarted the machine, that seemed to take care of it, even though I read somewhere else that it shouldn't fix font problems.
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