If I repair permissions twice in a row, without launching any apps or processes while I do this, the results are almost the same:
Why is it that the second time around, the problems seem to be encountered again?
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The errors with Safari are because -rwxr-xr-x should be lrwxr-xr-x where the l indicates symbolic link. I'm not sure how this is something to 'fix' from a permissions point of view as either something's a symbolic link or it's not. Repair Permissions has been removed in El Capitan so support for it with updated versions of Safari is likely to be overlooked.
The error about the InstalledPrinters.plist looks like a normal permissions discrepancy and I don't know why it wasn't repaired. The printer daemons may be resetting this.
It's normal for the ARDAgent error to be shown, as the error is included in this list by Apple of messages to ignore.