I have just updated my "C:\Mach3\macros\Mach3Mill\M6Start.m1s" code so that I will not use the G53 moves if all the axis are not Ref to home 1st.
Code:
  tool = GetSelectedTool()
  If GetOEMLED(807) Or GetOEMLED(808) Or GetOEMLED(809) Then
  MsgBox "One or more axis is not Ref to home, you will have to manually jog to tool change"
  Else
  code "G0 G53 Z0"
  While IsMoving()
  Wend
  code "G0 G53 X1000 Y500"
  While IsMoving()
  Wend
  End If
  SetCurrentTool( tool )