Newbie- ProtoTrax SMX g-code problem

[mech5107]

I'm an mechanical engineering student and as a project i need to use my school's workshop 3axis CNC machine, controlled by ProtoTrak SMX.
I have to say, that i have no CNC experience, exept some basic g-code writing and reading, thought during a class.
I'm using Catia V5R18, for producing the g-code, using various combinations of post processors, controller emulation and other options, but with no real success.
The controller manual write that the post of the ProtoTrak is very similar to Fanuc 6m, but there is no 6m post processor in catia.

Let me describe the problem...
Either way, producing a g-code file on catia, or writing my own (a simple one), i can read the code from the controller, and if i choose to view the toolpath, it's like the way i wanted to be, but when i try a trial run to test the program, the machine starts moving in the Y-axis, until it hits a limit or i stop it manual. Either if the first move is in X-axis Y-axis or Z-axis, it always make something not even close to the program.
The strange thing is that while running, the toolpath displayed does follow the right geometry (according to the design), but the X Y Z readings are following the "real" movement of the machine.

Hope you can realize the problem, cause it's a bit messy...

If i choose to make a simple mill operation, like an arc, or a straight line, directly using the ProtoTrak (from the various options of the controller) it does it perfectly.

Could you give me any advice? Does anyone knows the right settings of Catia for the ProtoTrak, or a general setting compatible with Fanuc 6m?
Any idea why the g-code input always cause the problem described?