John,
An older machine, with, I'm assuming, the original Logic Board. The Board may be starting to go; but as far as the permissions issue - I found with my own, older MBP (2008) that the issue started creeping up and Disk Utility wasn't always able to do a great job. I've always used DiskWarrior on extreme cases like this (or Drive Genius) and I find it does a much better job. The laptop runs smoother and there are less issues, and I don't have to run DU as often, if at all.
Also, if I were you I would be freeing up a little disk space. If you can keep 15% unused problems do diminish. Cross that line and issues crop up more frequently.
Finally, a complete Defrag (if you're backed up somewhere) would also help. I know we don't typically do this on the newer machines (isn't as recommended as it used to be five six seven years ago) but when I can spare the time to defrag a drive, it really helps. Drive Genius has been really great on the internal drives of my desktop, and has kept my library drives and my boot drives problem free for years.
Paul
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