I had what sounds like a simular problem when making the Negro Mods. where somehow MVPedit lost track of the numbers of batters that were supposed to be in a lineup.....this was certainly vexing, as every time i tried to correct the lineup it would revert back to only 8 batters. in fact it was listing my batters like 1,2,4,5,6,7,8,9 skipping the number 3. I believe what i did to fix this was to clear the entire team roster for the offending team. save. and then redo the lineup and save. if i remember correct.
Now if you are having a problem with EVERY minor league team, possibly you are experiencing something else. In my case, i had a problem with 4 or 5 teams. including teh vanilla comes with TC27 American League allstar team, which for some reason I was never able to correct.
hope I was able to help, but im not sure. it wont hurt your rosters for you to wipe the lineups and reset them yourself though.
But my guess is Genius Jim will be by soon and correct us all.