I checked teh DXF file it is fine , I checked the Gcode file it iooks ok, I converted the Gcode file back to a dxf and verified it is fine as well.
That eliminates the drawing and the Gcode.
That leaves the machine and mach3. Mach3 is NOT known to be wrong in its geometry. Are you running any FORMULAS in MACH3??
That leaves out of square machine, lost steps, Cutting deflection, Slow ACCELL for feedrate causing CV to compensate.
BUT you say you have veried the square and deflection and exact stop cuts the same.
NOW they ALL can't be right and it still cut wrong (;-). I would go back and check everything machine related step by step until you find the problem.
(;-) TP