Problem Weird g-code / cnc behaviour

Hello I own a CNC6040 bought from ebay
and I'm trying to realize some PCBs with it and EaglePCB (with pcb-code plugin).

I added three home switches (to zero the machine coordinates),
lights to the power/spindle buttons and the probe socket to the controller to do the z probing,
and I started milling a couple of rectangles of the same size/depth of my PCB into a piece of MDF.

The g-code was created online from the following link:
G-Code Tool Path Generator for Milling Inner Rectangles

To my surprise if I mill an outline of a rectangle everything is fine, but if I mill a filled rectangle
the x axis gets misaligned at every row, producing an overall misalignment of 2mm over 5cm along the Y-axis.
No problem seems to occur on the y axis alignment. I attach a low-res picture of the two results.

I'm using Mach3 on a Windows PC and I uploaded all configs, nc files and hi-res picture at the following link:
https://www.box.com/s/4avfosq38sitt7go4fh6

I'm stuck as I have no clue of what might cause this, any hint/suggestion will be greatly appreciated!!!

Kindest regards and
cheers from Paris!
Virgus

Attached Images

• 20130530_CNC_error_lowres.jpg‎ (53.0 KB)