@Cowboys3356: re: Missed Seasons: Are you using minor leaguers? I ask because if you aren't, you can use neutralized stats and that will fill in those gaps. However, if you are using minor leaguers, neutralized stats unfortunately cannot be used as the minor leaguers will import with horrible ratings (as there are no neutralized stats for minor leaguers and it would make for a ridiculously difficult undertaking for Spritze, Bigrod, and Markus who worked on the minor leaguers odyssey). Also recalc can help with this if you use 3 year or 5 year recalc. It can help to smooth out those 1 year bumps. I don't know how it would help with the war years though when players missed multiple seasons due to service time of a very different kind than being a baseball player.
The crazy good defensive ratings is a known bug that is hopefully being worked on. As for the rest, I'm not sure, but I did want to convey those potential workarounds for missed seasons to you.
EDIT: I see lukasberger beat me to it and was more concise. Oh well. Keep the Neutralized Stats thing in mind if you're not using historical minor leaguers, but DO NOT use them if you are.