7i92TM defect? How to verify?

Hello,
I would appreciate a second thought on an issue I experience with the 7i92TM. The board is connected to a G540. After installing linuxcnc 2.9 and some rearrangement of hardware, I only have two axis left functioning (z and y) and switches (connected to the G540) are not recognized anymore either. 
Swapping the wiring to other axis transferred the functioning axis over to the new config. 
I was suspecting the G540 to be at fault and swapped it against a chinese parport BOB I still had around.
After flashing the 7i92 with the correct file (5abobx2), the new setup shows the same behavior as before which pretty much rules out the G540. 

I am running out of ideas and hence considering the 7i92TM being the problem. 
I measured the voltage of Step+ to ground and Dir+ to  ground with Linuxcnc running directly at the BOB. Results as shown below. 

Xstep: 5V
Xdir: 0V
Ystep: 5V
Ydir: 5V
Zstep: 5V
Zdir: 5V
Y2step: 0V
Y2dir: 0V

Is my assumption correct that, since z and y axis do have 5V on step and dir an the others don't, that these are outputs are physically damaged?

Thanks for your help.