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Is it possible that some legacy monitoring software (virus checking or port monitoring) is preventing system changes?
I run the latest version of Little Snitch and the HSupdates went through OK with that active but older versions or virus checkers might cause problems.
I did notice that the update time was substantially different between a Macbook and an iMac but have no idea why - I thought the iMac had frozen but eventually it booted OK.
 
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