This needs verification from others (it may be my own error), but changing variables in the magiclantern.cfg file does not seem to affect the camera at all.
For instance, I was testing manual gain control, and found that if I changed Dgain to any arbitrary value other than 18 (say, 10), the display at the bottom would still read "Dgain 18/18," and my levels would be the same as if I had never changed the variable.
Trammell says that there may be a problem with the normal firmware overwriting these values as soon as they are changed. This may be the source of the problem. Once a simple menu system is integrated to change variables on-the-fly, this problem may disappear.