Heh....
I think the problem lies in the morale system. I was having the same problems with my deck gun crew till I told my cook to make a 'special' meal (glad I didn't have to eat THAT), and while morale remained high, the problems appeared to go away.
Now I use that 'crew obedience' or something mod, which lowers the morale requirement for commands.
http://www.subsim.com/radioroom/showthread.php?t=163091