Labels are how security contexts are associated with files and are stored as part of a file's extended attributes. If the system is started with SELinux disabled these labels can be inadvertently removed or become out of sync. A typical SELinux problem troubleshooting begins with a filesystem relabel to ensure that the labels are correct.
To relabel part or all of the filesystem on the fly without a reboot, see Section 3.2 and the fixfiles and restorecon commands. This is useful, but you can still run into problems with certain daemons by relabeling files without a clean reboot. Issue a touch /.autorelabel command to create the file /.autorelabel which will trigger the automatic relabeling of the entire filesystem during the next boot process.