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One thing to remember about RedHat/Fedora, don't use up2date, I have lost two fedora installations and one Redhat 9 install because of up2date. Always use yum, it actually works, and it does a fine job of updating and installing software.
As for Mozilla/Firefox, I can't pinpoint the problem based on what you said, but if I had to guess, it was probably due to up2date trying to update mozilla, and up2date crashed, so you might have to un-install and re-install mozilla and firefox, and all of the programs that don't work, and when you install them, if possible, do it through yum, just type yum install <package>.
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