Again after a long time spent trying to figure out how to export correctly Drill file for a squere pad this is the easiest solution.
Preface: on the PCB board you have a pad which is square dimensions 1mm X 5mm.
When you try to export it as a drill file you will find in the drill file the tool T011.000 but the dimensions and the routing path is missing.
I am still trying to figure that out why this happens, but the easiest work around is to export mill/rout file.
While looking at the drill file it seams like the x and y coordinates for the holes are there but the path from point 1 to point 2 was missing.
Hope this will help anyone.