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A bit of an update (and a work around).
Following the advice of Daniel Beck on the stackoverflow post above, I did 2 things to work around:
1: Restricted any usernames I added to lower case only.
2: When logged in with full permissions, I made sure I saved the 'configure system' page (even though there were no changes).
I don't know if both were required, but I now have an instance where permissions will persist after restart.