I recommend that you manually change the user and group IDs (UID & GID) prior 
to upgrading the system.

On the old system:

usermod -g 1000 username
usermod -u 1000 username

Then run:

chown -R username:username directory
chgrp -R username:username directory

for all of your directories.

Reboot and make sure everything is ok. I had to redo one or two of the 
commands, for some reason, after rebooting. Maybe I didn't chown/chgrp -R 
everything correctly.

This worked perfectly for me when I migrated from Fedora 15 to Fedora 16.

I hope this is what you needed.

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