I think the problem we were having was in the "complete depth chart" part...
For example, in one game my starting shooting guard fouled out early (after 17 minutes!!) and my back-up SG was a horrible player. I had no reserve for SG, cause I wanted only those 2 guys to play as SG. But then I guess the game engine considered my depth chart incomplete and looked for another player that could fit in the reserve SG position that was blank. And that way, instead of my horrible backup SG, my starting Center(that was resting in that game as a Reserve center) ended up playing 28 minutes as a SG.
So I guess what we have to do is to always submit the depth chart complete, with no blanks. The trick to order only 2 players to rotate in one position is to repeat the name of one in the reserve position, or to put any scumbag as a reserve, but never leave it blank.