If I had to guess, I'd say there's a marginal RAM, that maybe isn't being caught by self-test (if you aren't hearing any RAM error beep codes in self-test).
RAM errors are not displayed on screen, it's only audio tones. But you can get cases where a RAM that is on the edge won't be flagged in self-test, but can still be bad during gameplay. The best way to test it would be with a Fluke or Catbox, that can stress test the RAM over many loops.
You could also maybe try lowering the board voltage from 5.0 to 4.8 or 4.7V and see if self-test throws any RAM errors, as a healthy board should still work down to 4.7V with no errors.,
Definitely a weird one. Can't say I've seen this issue before.