All the files are backed up but i think its the same schedule whatever.
That seems very unlikely. I mean, there's some randomness, it's not the same schedule year after year. So unless the randomness is based on some unchangeable seed in the saved files, why wouldn't it be different on a subsequent generation?
I've noticed similar 'qwirks' in Davids league where a team might play the same team home/away in two weeks.
That's wonky, but not totally unprecedented. I'm pretty sure the World League did it. True, it was in the 6-team configuration so it was harder to avoid, but it's nothing I would say must be avoided. The crossover repeating seems like something much easier to avoid. Again, is there any way to designate that the other conference's 5-team division should have the crossover team in a given year? That seems like the best solution and would shake things up a bit.