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The Metamachy games from the tournament don't seem to be affected by this. Perhaps because the matches were assigned.

I just tested this, and assigning games didn't make a difference. I assigned fergus to play White and duniho to play Black. It correctly assigned $players to "fergus duniho". When I went to make the first move, it was for fergus as Black. After making a few moves, I had duniho resign. The comments on the last line say "// - Gus Duniho has resigned. -// - Fergus Duniho has resigned. -" and it reports that Gus Duniho (who is duniho) has won.

While looking into this, I did make one change that may have made a difference. The form_assign.php script didn't previously create a $players string, which meant that assigned games were not using the value of this string to determine who is who. That might account for why games in the tournament were unaffected.

One solution, which I started working on yesterday, is to write a new settings file that makes the White player manually pass the first move instead of automatically adding the move for White and letting Black make the first actual move. This would make the first move actually belong to White, which would stop it from mistaking Black for the first player.

Alternately, maybe I could make sure that color choice is preserved and not assume that White moves first just because it is first in the $sides string. The $players string is newer than the $sides string, and I expect I'm not using the $players string everywhere the $sides string is used, which leads to a discrepancy between them in instances where Black ends up moving first because White's first move is automatically passed.