The maximum speed of homing moves is much slower than for printing moves, because the endstops have to be checked. So if you use high microstepping, you need to use slower homing speeds. The 1.21RC firmware should allow slightly faster homing than previous versions did.
To check whether you are trying to home too fast for the microstep setting, first make sure the printer has a long way to go to home, then run M122, then home it. Then run M122 again and check the MaxReps field. If it is higher than about 50 then you are homing too fast.