Patience,
I think people here are losing that because all that was asked for was the g-code file that went with the pen output you showed first. Instead you are doing everything but what was asked and you are getting no closer to the answer.

The gcode was posted in reply #16

patience,
The xml file is lacking basic configuration information  like motor tuning, ports and pins definition, etc, thus it is useless!
Please post the xml file you are using. When you open Mach3 you will see the name of the file next to PROFILE:________
on the main screen. You will find the xml file in the MACH3 directory.

RICH

patience,
The xml file is lacking basic configuration information  like motor tuning, ports and pins definition, etc, thus it is useless!
Please post the xml file you are using. When you open Mach3 you will see the name of the file next to PROFILE:________
on the main screen. You will find the xml file in the MACH3 directory.

RICH

The file Igecko.xml that is at the link below is the profile file.  The table is set up with an Igecko driver box, so he named the profile "Igecko".  The Igecko.xml that is posted in the share file below is the file that contains all the port and pin data.

https://drive.google.com/open?id=1uwvsEUVPyV0TQtdnZtBcp3AsVNUf-65x

Patience,

Note that if you reference your machine / home location defined to the Mach3 as 0,0,0 and that location
is the basis for the programs gcode then machine coordinates and program coordinates are the same. No
G54 / part offset exists.

I checked the gcode and found nothing wrong with it. I ran the gcode in Mach3, numerous times.
Ran the code the first time, rewind the code, and cycle start it again, NO PROBLEMS  on my end.

Your program code explained in a simplistic manner.
A move will be made  to the start of point of the first lead in to make the bottom hole line N0120.
N0120 X6.6757 Y3.0713
Then a move is made to next lead in for the next hole and so on until all the holes are cut. Then there is a move to
a lead in for cutting the rectangle clockwise, ending with a lead out /  line N0940.
N0940 G03 X11.8677 Y25.6713 I0.0000 J0.0960

Doing nothing else after running the code the first time, rewind the code, cycle start, the controlled point should move to X6.6757 Y3.0713. There should be no offset like you have shown. To check that, put a dwell / add a line of code  " N0125 G04 P10" after line N0120 since that will give you approx 10 seconds of no movement and you can look at the X & Y DRO's to see that  the DRO values match the code values. Do the same to check the location of the  last lead out. Add a line of code  " N0945 G04 P10" after line N0940.

UNDERSTAND THE FOLLOWING:
You are not using the default Mach3 screen set, and your xml file can't be used for  anything by anyone because
you have a custom screen set and may even be using a customized version of Mach. That said, unless someone has the exact same "system" as you it will be fruitless to try and duplicate what you are doing. So you are on your owne. I prefer not to guess what the problem or cloud the issue.  

Good Luck,

RICH

Patience,

Note that if you reference your machine / home location defined to the Mach3 as 0,0,0 and that location
is the basis for the programs gcode then machine coordinates and program coordinates are the same. No
G54 / part offset exists.

I checked the gcode and found nothing wrong with it. I ran the gcode in Mach3, numerous times.
Ran the code the first time, rewind the code, and cycle start it again, NO PROBLEMS  on my end.

Your program code explained in a simplistic manner.
A move will be made  to the start of point of the first lead in to make the bottom hole line N0120.
N0120 X6.6757 Y3.0713
Then a move is made to next lead in for the next hole and so on until all the holes are cut. Then there is a move to
a lead in for cutting the rectangle clockwise, ending with a lead out /  line N0940.
N0940 G03 X11.8677 Y25.6713 I0.0000 J0.0960

Doing nothing else after running the code the first time, rewind the code, cycle start, the controlled point should move to X6.6757 Y3.0713. There should be no offset like you have shown. To check that, put a dwell / add a line of code  " N0125 G04 P10" after line N0120 since that will give you approx 10 seconds of no movement and you can look at the X & Y DRO's to see that  the DRO values match the code values. Do the same to check the location of the  last lead out. Add a line of code  " N0945 G04 P10" after line N0940.

UNDERSTAND THE FOLLOWING:
You are not using the default Mach3 screen set, and your xml file can't be used for  anything by anyone because
you have a custom screen set and may even be using a customized version of Mach. That said, unless someone has the exact same "system" as you it will be fruitless to try and duplicate what you are doing. So you are on your owne. I prefer not to guess what the problem or cloud the issue. 

Good Luck,

RICH

Rich,
Thanks for giving it a shot.  The custom screen set up is based on the product CandCNC sell.  Being the GCode all looks good, then I suspect my issue is in the actual hardware or communication between the computer and table.