Why does "repair permissions" actually creates more repairs when again.

When I use Disk Utility repair permissions, I run it a second time and there were more instances than noted in the initial run. 13 the first time and 22 the second. To double check, I rebooted my MBP to make sure it wasn't an issue with a running program. The same thing happened, I got 13 instances the first time and when I hit it again, I got 22. I find it hard to believe that by running "repair", more instances are created.
Also, why are some things just not repaired?
Thanks so much for any guidance.
Sincerely,
Skip

Specifically, what "repair permissions" does is look at a bunch of files called "BOM files" or "Bill of Materials files", which is simply a list of what files where installed where and with what permissions. They are created by the Mac software package make that vendors use to build installation packages (if you've ever installed software that required you to run an installation program rather than just copy it to /Applications, that's what you have).
When you run "repair permissions", it compares the file's permissions with what's in the BOM. If they aren't the same, it changes the file's permissions to whatever the BOM says they originally were. The idea being that something might have altered the permissions on a file file making it impossible for you to access and thereby messing up anything that requires access to the file. In practice, that doesn't happen too often.
What does happen pretty often is that the software installer copies files and then changes permissions on them. Even the application may change permissions on the files. That's pretty common, and often necessary to the operation of a piece of software. So, despite doing a "repair permissions", some files and directories are going to simply defy having their permissions modified (particularly things like directories where log files are stored).

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