Volume corruption may cause permissions problems in OS X
If permissions are regularly changing and your system is slowing down, problems with the hard drive's formatting may be to blame.
One of the key components that needs to be working properly for any system is the primary storage medium (be it a hard drive or SSD drive). If the system cannot access files from the boot drive then you may experience slow-downs, errors, hangs, and crashes. Usually provided the hardware and file system format are working properly these errors can be addressed with a permissions fix, a general maintenance routine, or even an OS installation (which is fairly seamless with OS X); however, if there are problems with the file system, then the fix is not so easy.
If your system is regularly getting slower and slower despite attempts to clean out the system and fix permissions, then you may be experiencing problems with the hard drive or the file system formatting on the hard drive. The best way to test this is to run a drive verification with Disk Utility or preferably with another more robust drive management tool such as Disk Warrior, Drive Genius, or TechTool Pro. This will show you if there are any problems with the directory structure on the drive or the drive hardware itself, and if these problems can be fixed.
The HFS+ format in OS X is essentially a few hidden high-performance database files (called "b-trees") on the hard drive that hold information about where items are physically located on the hard disk, along with some key attributes about these files including user ownership and permissions. If there is an error with one of these database files then the system may get confused as you use various system files, and start changing these attributes around, ultimately resulting in regular permissions corruption or other odd behaviors.
To clear this problem, run a permissions fix on the boot drive and then back it up as soon as possible using Time Machine or a cloning tool. In addition, try manually backing up your documents and data to an alternative external drive to ensure they are safe.
When this is done, boot the system to the OS X installation DVD and launch Disk Utility from the Utilities menu after choosing your language. In Disk Utility, select the drive device (not a volume under it) and click the tab labeled "partition." Then select "1 Partition" from the Volume Scheme drop-down menu, format the volume to Mac OS X Extended (Journaled) and apply these changes. The disk will be completely formatted and set up with a rewritten partition table and volume structure files.
When the disk is formatted, quit Disk Utility and then select "Restore System from Backup" from the bottom of the same Utilities menu. Follow the onscreen instructions to restore the system from your latest Time Machine backup, or if you have cloned your system, then boot to the cloned drive and clone it back to your main boot drive.
After the data and system have been restored to the drive, restart the system and ensure that all of your data is as it was when you backed up, and then run another permissions fix using the Disk Utility program that is on your internal drive. This will ensure that the permissions are set according to the most up-to-date permissions database for your system.
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