1) You ARE saving the changes you make in the ACE, aren't you?
2) Does your OS (Vista or Win7) require you to run ACE "as an administrator" so that the saved changes can be made to the aircraft.cfg?

Mark

@Pinatubo. I often make the changes while I'm actually using the aircraft in FSX (accessing the Captain Sim > 767 ACE from the menu). I just reload the aircraft and the changes have been made. It always works for me.