Just in case anyone else hits this problem, I found the cause.

My ~/.local/share/applications/ directory had a compiz.desktop file in
it.

Don't know what wrote the file or tried to figure out exactly what in
the file caused my "Visual Effects" settings to get messed up on login,
but my other systems don't have this file and I simply renamed it to get
rid of the problem.

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Appearance "Visual Effects" settings lost across reboots and log out / log on
https://bugs.launchpad.net/bugs/500570
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