Protesting a game after it is complete

Question
Dear Dr. Mark,

Our Church league team won in extra innings recently, only to find out that the other TEAM protested a call on the field.  The call was that the hitter who hit a homerun didn't step on home base.  We appealed the run and the umpire called the batter out and that the run didn't count.  At the time, one of the players started to argue with the ump and he told the player to very clearly let it go the ruling stands.

Fast forward a few days after we won this game in extra innings...the commissioner of our league now wants to start the game over from the time of that call because the other team is now protesting the game.  They did not play the rest of the game in protest, but protested the game after the game was complete.  The commissioner says that we need to play the remaining innings again, as the ump's ruling violated ASA rules.  I don't know if this ump as ASA certified or even trained.  Our league doesn't have that requirement.

I think that this is completely insane.  Am I losing it or is the commissioner for suggesting that we start playing the game again, as the other team lodged a protest once the game was over and we were the winners??  

Answer
Sorry Patty,

The LD can do pretty much anything they want.

However in ASA you cannot protest if a runner touched a base or not (9-a-5).  I do not see anything in your facts where the umpire violated anything, something I'm missing or you didn't tell me?

Plus if you protest a legitimate mis-application of the playing rules it has to be made right after the call and both teams informed the game is being played over protest.

Mark