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Raw counts will be set to 0 when LinuxCNC starts so its still
just a relative count number.

What is the spacing between index marks on your scale?

You have

setp hm2_[MESA](BOARD).0.encoder.00.filter 0

(on all axis) You might try:

setp hm2_[MESA](BOARD).0.encoder.00.filter 1

In case it's a noise issue.

Yeah, sorry, I copied them from a 7I96S halshow and forgot to delete the "s"

Thank you very much, I will try those fixes and get back to you.

I also wanted to mention that when we manufacture this machine with new pc hardware and this new software we get the latency warnings but the machine performs without issues. I don't know if that is relevant or not.

Fixed the outputs and inverts for 7i95t, 7i96, 7i96s, 7i97 and 7i97t.

JT

Yes, that is the BOB with very slow optos, and as long as you get latency warnings, the steps might and will be missed, so
-Set the base period to 100000
-set the drive microstepping to 1600
-set the parport reset time to 10000 in the hal file
-set the step time and space to 10000 in the ini
If you still get latency warnings, in BIOS:
-disable hyperthreading
-disable TPM
-disable "aggressive PCI-E power something or another"
-disable any power saving option, like C states, turbo, speed step, etc