Transform problem

Hello, I am having a problem cutting multiple parts using the transform function in SolidCAM. It looks to me like the problem is post processor related. Something goes wrong when transforming to the next part.
I attached the program I am trying to run (FT45012R01_3_set.txt). This part has two different drills and bunch of contouring operations. The drilling cycles go just fine, and most of the contouring cycles also go fine but when it gets to the mill (tool#1) I get a soft limit warning on MAX Z so I turned off soft limits to get going and ran into the limit switch. I don't understand what is wrong. Could it be that - the code is telling Mach to go positive on the Z axis when it only can go negative?
I ended up recalibrating the tool #1 offset and using run from here which worked for some reason but the calibration was wrong and one of the parts was ruined.
I made another program for the two good parts that were partially cut (ft45012fix.txt) this file picks up after the drilling cycles. It cut the first part fine and moved one to the next part starting cutting it and all of the sudden decided to turn left instead of right and ran into previous work ruining it.
So after the tool ran into work I wanted to see where is was trying to go, I raised the tool and hit start, it just when off way out and was cutting strange circular shapes, but then got to the next transform step and got back to proper coordinates.

Another strange thing happened when I was getting ready to run the “fixing” program on the two partially cut parts. I used my probe which always worked fine but when I tried using to find the edge it touched the edge and reversed direction and did a rapid move for few inches before I stopped it. I decided to restart Mach, doing so made the probe work as expected.

When I watch the toolpath on another computer in the office I see that when the transform occurs, the coordinates abruptly shift but the tool path displayed cut in the same place for all three parts that I have in the array.

Is there something in my programs that is causing these problems? I see that G90 is absolute coordinates command which seems to cause the abrupt coordinate shifting described earlier. Do I need to add something to my initialization string?