Hmm, I'm not seeing that. I just set a specific collapse order, saved it as a template, cleared the tables, loaded the template, and the collapse order was correct. Then I saved the tournament, created a new tournament (to clear everything), loaded the tournament, and the collapse order was correct. I set this tournament as the "default" tournament, exited and restarted the TD, and the collapse order was correct.
Let me know if you find different.