5i25 to 7i92TM - Spindle Index No Longer Working

Hi Guys,Recently I had my 5i25 card fail and bought a 7i92TM to replace it, updating my HAL file to suit the new ethernet board.
LinuxCNC runs as normal, however, the spindle index pulse is no longer being recognised. The index pulse was detected and rigid tapping worked when I had th 5i25 card installed. I have not made any changes to the HAL file in regards to the encoder.

I confirmed with an oscilloscope the encoder is outputting the index pulse.
Halscope will detect the A and B pulses but not the index pulse.
The index pulse is not detected in either LinuxCNC 2.8.0 nor 2.9.4 (rigid tapping just hangs)

Is there something I am missing in my HAL file or is there a timming error in which the encoder pulse is not being read by the 7i92tm? 

I would first verify that you have the correct firmware installed
in the 7I92T (7i92t_7i76x2d).

Next, I would verify the hardware by setting the 7I76 index input
mode to TTL mode (W4 left), unplug the encoder, then watch
the signal hm2_7i92.0.encoder.00.input-index in halshow
and check that it changes state when you ground the IDX+ input
(TB3 pin 13)