Problem while switching coordinate systems.

 
Hi guys,
Recently i've discovered a problem in my machine, it is about switching between coordinate systems. I described my steps below.

1. I am taking zero of the piece with assigning offsets by G54 command.
2. I am processing the first face of the piece. When it comes to second face, the A axis need to be turned. After this turn, i am changing the coordinate system with G59.3 command. As result, the offset Y is being swapped with Z offset. This is when problem shows up. The swapping operation is being made with 25.4 times the previous offsets. I am giving an example of the situtation below.

Here is the offset has been set before processing 1. face of the piece.
--> Y: 50mm
--> Z: 20mm

Here are the offsets generated before processing 2. face and after G59.3 command in Y an Z axises.
Y: 508 (which is previous Z offset multiplied by 25.4)
Z: 1.270 (which is previous Y offset multiplied by 25.4)


I've checked the .var file in my system and i've discovered that linuxcnc actually puts the values multiplied by 25.4. Here is my question, is there any relationship or operation that i need to do before switching coordinate systems? 

I am attaching my G-code.

Thank you for sharing your knowledge.

Berkay.


 My GCode goes like below:


%
(AXIS,stop)
(1234)
(ISO)
N10 G21
N15 G90 G94 G40 G17 G91.1
N20 G53 G0 Z0.
(FACE2)
N25 M5
N30 G53 G0 X63.5 Y63.5
N35 M0
N40 T37 M6
N45 S8500 M3
N50 G54 G0
N55 G53 G0 X63.5 Y63.5
N60 G0 A90. B0.
N65 M254 P9
N70 G59.3 G0
N75 G43 H37
N80 G1 X43.11 Y-1.309 F5000.
N85 Z9.
N90 G1 Z3.
N95 Z0.3 F100.
N100 G18 G3 X42.71 Z-0.1 I-0.4 K0. F300.
N105 G1 X-2.51
N110 G17 G2 Y-0.129 I0. J0.59
N115 G1 X42.71
N120 G3 Y1.05 I0. J0.59
N125 G1 X-2.51
N130 G2 Y2.229 I0. J0.59
N135 G1 X42.71
N140 G3 Y3.409 I0. J0.59
...
...