One system-config-securitylevel is creating a file /.autorelabel. Which causes the relabel on the next
boot. So if you want to relabel your file system you can just create this file and reboot. It will run the
fixfiles in "single user mode" and then boot up in the current policy. Not sure if it will work correctly
coming from an upgrade of fc2.
system-config-securitylevel, is not supposed to touch the firewall stuff unless you modify something on the
front screen. There are a series of checks on the OK button to only apply changes if something changed, so
I don't see how the firewall rules got effected by changing SELinux page.
Dan