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I have experience a similar issue when using ReiserFS as the file system. When I used ReiserFS, some fonts, libraries, and programs were lost. Also GDM can corrupt some files. Now I use XFS for the files system and KDM for a display manager and I do not have any problems. To minimize any bad shit, I use ECC memory.
All you can do to fix the issue is install the lost data and reconfigure. A full install is not needed. After you make all the changes, use the sync utility to make sure data is written to disk.
I think Fedora comes with hardware detect software (I think kudzu or something similar) that might be giving you problems. Try using chkconfig to turn off desire scripts for all run levels.
It dumps the cache data from memory to disk. Use man or info to learn more about desire programs. Some programs may not have any man files, so you have to include --help or -h when running the program.
Google does a better job searching forums and several other web sites than site's built-in search engine. To make searching for information using Google easier, a book title "Google Hacks" from O'Reilly is good.