How to repair a hard drive that Disk Utility and Disk Warrior can’t fix

Usually, you'd ignore the problem. It just means that contradictory permissions are specified for those files. It can't satisfy all of them at once.

In Mac OS X v10.5 or earlier, when you verify or repair disk permissions Disk Utility reviews each of the .bom files in /Library/Receipts/ and compares its list to the actual permissions on each file listed. If the permissions differ, Disk Utility reports the difference (and corrects them if you use the Repair feature).

Source: About Disk Utility's Repair Disk Permissions feature

The problem here is that different receipts specify different permissions for a file. If it sets them one way, they're wrong according to the other.

I think Apple used to mention possible contradictions in permissions, I'll see if I can find it.

But in your specific case:

Looking at the specific permissions in your log, I doubt this applies to you. The d indicates a directory, which means a file has been replaced with a directory. Fixing permissions is not going to fix this; it can't transform the directory back to a file.

I suspect this would be fixed with a reinstall. I doubt the disk needs replacing, however.

Most of the difference you're seeing is due to Time Machine's "Local Snapshots" feature. When Time Machine is turned on but the backup device isn't available, it backs up to the local volume. The space used for these local snapshots is counted as "in use" by Disk Utility and System Information, but not the Finder (see the Disk Space considerations section of this article). While the space for backup actually is in use, it'll be freed automatically when needed (i.e. when the volume gets above 80% full), so the Finder counts it as being available.

In your particular case, the space System Information lists as being used for "Backups", 98.36GB, is very close to the difference in free space listed by the Finder vs. the other two. The Finder's 206.43GB free - 98.36GB of backups = 108.07GB actually free; compare to System Info's listing of 108.44GB free and Disk Util's 108.31GB. I'm not sure what the rest of the difference is (maybe they looked at the disk at slightly different times? Or they may be counting volume structures a bit differently?), but it's very small.

Finder shows:

• easily, the truth for JHFS+ volume Macintosh HD
• optionally, the truth for mtmfs volume MobileBackups

Hint: with local snapshots enabled in Time Machine, in Finder you can go to /Volumes/MobileBackups then get info.

Results of a one-line command show that for some purposes, MobileBackups is treated as a distant file system:

qlmanage -m disks | grep MobileBackups && mount | grep MobileBackups

As Disk Utility is oriented to local file systems, we'll probably never see MobileBackups as a separate volume in that context. There are degrees of simplification in Disk Utility, even when debug options are chosen.