Shah,
Not real familiar with the 0-5 version but the control should be the same as mine. I have a partner 1 and a partner 6 VMC's. Mine have 3 switches on each axis, 1 home switch and a plus and minus limit switch. It sounds as if your parameters were rewritten to speed up the homing process which may cause the axis's to over shoot the home switches. If the axis overshoots the home switch it may be hitting the hard limits then you'll have to manually turn the screw (with the power off) to get it back on the other side of the limit switches and past the home switch. Be careful that the switch arms don't get bent in the process of doing this. Check the switch arms and make sure they are straight, not bent into a U shape.
Dave