Newbie: Two halves of simple die not aligning properly - Long

Very new to both the software and the machine and trying to learn
where to start the troubleshooting.
I have a Shopmaster Elderado Bridgemill (3 in 1).
I use Mach2 and Sheetcam.
The machine is calibrated well with Mach2 (~.002 after several X and Y
commands then return to zero).

I have created (for testing) a very simple DXF file that contains 3
drill holes for indexing, a horizontal line as well as one vertical line.

Half A:
I import the dxf file into Sheetcam, create the drill gcode for the 3
holes, save the file and then create the mill gcode for the horizontal
and vertical lines and save the file.

Half B:
I then use the same dxf file and select the horizontal MIRROR option
and repeat the above processes for creating the other half of this
simulated die and save the files for half B.

I then open Mach2, load the Gcode for the drill (indexing holes) and
run the program (this is after indicating the workpiece in the vice
and setting zeros on all three axises). After the 3 holes are
drilled, it returns to zero, I remove the drill bit and replace with
an end mill and reset the z axis zero (x and y are still the same).

I then load the second half into the vise and indicate the corner to
zero just like I did with the first half. I load the "Half B" drill
gcode, let it run, it returns to zero and I change the drill bit out
for an end mill and reset the Z axis zero. I then run the mill
process for half B.

When I put the two halves together, the index holes line up properly
but the two milled slots are slightly skewed from each other (approx.
1/8" over 4" of travel).

I thought sheetcam was causing my error, so I created half B using the
mirror command in Autocad and got the same results after running each
dxf file through sheetcam.

I don't understand why the 3 randomly spaced index holes line up fine
(put pins in the holes and can put the other half over the pins - no
slop in the holes or pins) but the milled slots are skewed. I would
have thought if there was an error in the travel of the machine, that
the index holes would reflect this as well and they would not line up.

Does this make sense?

Where is a good first place to start looking for what is causing my
error?

Thanks,
Jim