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Some of the cheaper fixed bearing blocks are sold with non angular contact bearings, this is something to check.
Until you perform a backlash test, and yes this can manifest as repeatable, you can not rule out a mechanical issue.

Thanks Rod. I'll look into upgrading to 2.10.

Good to hear. I'd suggest slowing down the SPI comms like in the discussion above.

hal
loadrt remora-spi SPI_num=0 CS_num=0 SPI_freq=2000000

ini
#SERVO_PERIOD = 1000000
SERVO_PERIOD = 5000000

Did the subroutine execute?

You could run

halcmd show signal s-index-zero-for-ATC

From the command line to check

No, the actual index pin is not typically used by LinuxCNC

What interface card are you using for the encoder interface?

Is the encoder single ended or differential?

Is  the interface card jumpered to match the encoder type?

Another way to check the low level hardware is to set the index input to
single ended mode, and then watch hm2_7i80.0.encoder.00.input-index
in halshow as you ground the index input on the interface card.
hm2_7i80.0.encoder.00.input-index  should change state when you ground
the +index input pin

(with the encoder unplugged of course)