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Slow optocouplers.
Better quality BOB should help, or just get 2 fast optos.

My lathe spindle originally had an Index pulse and 10 encoder pulses per revolution. From the problems discussed in
      forum.linuxcnc.org/38-general-linuxcnc-q...peed?start=40#319800
I thought it would be better if I generated more than 10 pulses per spindle revolution.

I built a ring to fit on my lathe pulley with 180 teeth. I picked this size because it had the most teeth that I though I could machine. They were about 1/16" width and depth. I found that the proximity probe I was using could not detect these small teeth. I replaced it with a Hall Effect Sensor =11.0ptS38J-22ADSO-5KJA5 from Standex Electronics. Here's the installation:
 

Here's what the output looks like at 400 RPM on my oscilloscope:
 

This is about 24V. The frequency of the signal is about 6 cycles in 5 mS, or 1,200 Hz. Expected signal is 180 pulses * 400 RPM / 60  = 1,200 Hz. So far, so good.

The signal goes into a breakout board with optoisolators. I can see the signal on the input and output side of the optos, so I know it's going into the circuit OK. I don't see any missed pulses on the oscilloscope. The breakout board feeds a Mesa 7i92.

When I pull up the encoder inputs in HalScope, I see:
 

Not good. I should see 180 pulses between the index pulses. I'm seeing about 10. Plus, one of the index pulses is missing.

I have a separate DRO that also displays the spindle RPM. If I compare it to the RPM shown on LinuxCNC, they match from 0-150 RPM, then for higher speeds LinuxCNC shows speeds lower than 150.  So if the lathe is at 500 RPM on the DRO, LinuxCNC shows about 60 RPM. Again, I can see on the oscilloscope that I'm getting all the pulses.

Here is my .INI and .HAL files. Any ideas?