permissions on /etc/localtime drwxr-xr-x should be lrwxr-xr-x
The initial d vs. l jumped out at me. After the repair, when the setting still didn't stick, I went into the terminal to have a look. I found a directory in etc named localtime and it had a file named Eastern in it -- not knowing how the data should actually be stored, this seemed reasonable to me. I deleted the file named Eastern, but that didn't fix it. Then I deleted the entire localtime directory. That worked.
I assume that some time in the past Apple stored the timezone in a file in this directory, and whenever this system was updated, the updater failed to remove the directory.
The moral of the story: pay attention to the items that Repair Permissions throws at you.
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