SH3 commander problems

[orangehat44]

We'll they arnt really problems persay, but I am having non conformities with certain things with SH commander. I create a captain in sh3 cmdr and load it and the commander profile is in the game and sh3 commander does keep track of it but a list of things dont occur:

1.) it is suppose to skip the intro movie but it still plays everytime I load.
2.) This is the big one, I have set cmdr to use no fatigue model, yet I am still getting to points when my effiecinecy drops to a certain point I cant operate compartments, so it appears I am getting effected by fatigue.
3.) if I set a uboat number in commander I get a different one in the game.

There may be other small ones I cant think of atm but I do get these inconsistencys and dont understand why. I followed the directions to the t. I do have a steam version of the game I dont know if this affects the mods I install and could cause a problem. I still love commander for the things it does do when I tell it too, but it would be great if I could get it to do everything its suppose to. Especially the fatigue, I was thinking of playing a campaign without fatigue to learn the ropes then another time do one with fatigue on. Problem is when I assume fatigue is turned off it usually gets to a very unopportun time for me to realize it is off like when Im tryin to evade and realize Im not moving because my engine crews are exhausted.

Any tips?
Thanks