You may need to modify the Ref All Button Script. Go to OPerator >Edit Button Script, and click the Ref All button. The script should be:
DoButton(24)
DoButton(22)
DoButton(23)
If that doesn't work, try:
DoButton(24)
DoButton(22)
RefCombination(10)
Make sure the "Home Slave With Master" is NOT checked, and restart Mach3 after making any changes.