Q: Ongoing permission repair problems --- is there  a way to prevent or limit them from happening?

The best thing for you to do is stop repairing permissions unless you are getting permissions errors relating to system files.

You are presently getting what sound like recurring but innocuous messages you can safely ignore. But unless you post something here to see, we have no clue what you are seeing.

In addition to the excellent explanation already given....

see > Mac OS X: Disk Utility's Repair Disk Permissions messages that you can safely ignore