I've noticed that Conferences with Divisions and the 12b Conf Tourney type setup, don't seed properly. I had this happen:

Florida Gulf Coast 12-4 record (East Division Leader): #2 seed in conf tourney

Bellarmine 11-5 record (West Division Leader): #1 seed in conf tourney

FGCU was better in conf record, overall record, and NET . And the rest of the seeding was all off a little bit too. I checked a different conference that uses the same format and they had a different order as well.

Conferences with 12a tourney setup seem to have no problems.

I will double check but I am pretty sure that the code is set to seed by division so being the #1 or #2 seed is irrelevant as they are technically both a 1 seed (1 East and 1 West) and the game just is choosing the West to be the #1 and East to be #2