Index pulses

I don't think this has anything to do with m19
(that's just a GCODE hook to start and wait for orientation)

Looking at the orient component, it basically rounds the current encoder
position-offset to an integral number of turns and then adds the orientation offset
so should never unwind/wind more than 1 turn (or 1/2 turn in mode 0)

You probably need to take a look at the orient "command" vs the encoder position
to debug this, they should never differ by more than 1 turn.

Note that they could differ by more than a turn if you started an orient operation
when the spindle was still spinning.

PCW, you may be interested, I made a modified encoder counter (with an additional register to offset the index position) for hostmot2.
This can be used for multi-start threading without offsetting the Z axis.
Modified driver only for 2.7.15, vhdl source code taken from hostmot2.zip(dated 150220).