If you are performing your break in, you are not running the car down the road @ high speeds. The motor is still at the factory settings witch will be really fat, so fat to the fact that you should have to empty out the tunepipe before you can start it to evac the excess oil. So have you leaned the air out yet ? What step of your break in did you notice your diffs being hot?

My money is on the motor warming everything up, unless you put the vehicle on a brick which will decompress you suspention and put the shafts at an angle which may cause a lil heat but not much. Do you Have greased difs or oil sometimes grease in front and oil in the center and rear. Do you have aluminum dif cases or plastic.

Give us just a lil more info.