@acbeer
I feel your pain... The exact same thing happened to me on my second season and I dedicated so much time to that playthrough.
I played 50 - 60 games in the first season and was game 19 in the second season when all of a sudden... SMACK DAB BLAMO and then nothing... nothing was happening, just a frozen screen. no matter how I tried, even when I choose to play the game that was causing me problems, when the game was over it froze on the next screen. So I don't know about the whole not the same amount of players on the minor league team thing. I could play the game fine, it iis as SOON as it was over or if I tried to sim it. ALWAYS the same thing... FREEZE RAY hit my screen...
In the end... I reinstalled everything and updated to the latest rosters and made sure I had all the current Stadiums, the Updated global.iff, as many faces and portraits that my sanity would allow, and started again. This playthrough I decided to go strictly Manager mod, cpu vs cpu for all games and I never had a crash or frozen screen. I simmed all the way up to the all star game, every game I watched or at least had it played out at real time. 80+ games and I didn't have a problem. I was testing a new datafile that I concocted out of the plethora of datafiles on this site. I learned so much and created what seems to be the most realistic statistically speaking games. I am in the midst of gathering data and posting my results with EVERY action I took pain painstakingly written down. As well as a comparative datafile template to show others what I changed. Long story short...
... Sorry dude... no answers... never figured why that ever happened. Only that it happened to me the same way also.
Best of Luck.