The only thing that I've seen that messed up a macro was E Stopping in the middle of a macro. Sometimes subsequent macros will no longer run correctly. So always restart Mach3 if you estop in the midle of a macro.
The only thing I can think of would be a bad .xml file. I'd try creating a new one from scratch and see if it still has an issue?
As you said, there's nothing in the macro to move the A axis, so I don't know what could cause it.
As for your zeroing method, there's a much simpler method. On the toolchange tab, enter 3.813 in the Material Offset DRO, and check the box. Then Zero to the table, and the Z zero will be set 3.813 above the table in one step.