Are you sure it is repairing the permissions and not just listing differences that are not actually repaired?
Please try repairing permissions again and seeing if that long list is still there.
No, I don't know what was actually repaired, and I haven't yet repeated it to get an impression, but I'll do so later today. As it happened, after the OS update & permissions repair I ran into an unrelated snag that sucked quite a bit harder (and more successfully) at my time... I'm aware of your position on the issue you describe, and was surprised that you actually ran the repair yourself anyway.
