I think it is time to put a scope on the encoder. it sounds like there may be a big duty cycle or phase angle error in that encoder. In other words, at constant speed, the 4 quadrature transitions are not evenly spaced, but at least one of them is out of time.
I can see the phase angle errors in halscope by looking at the measured velocity at low speed. There is a regular 4 step cycle. I can see the same effect on the other encoders, though it is not as pronounced. All encoders have some phase angle error but I have to admit this one is worse than I would like. The problem is compounded by it being a fairly low resolution encoder. However this does not explain the occasional big spikes, especially the example where I had a spike of zero velocity for one count. The machine was moving at low speed so I could see individual counts in Halscope. To read zero velocity that count should have been MUCH wider than the others and it was not. There has to be something wrong with the the way the velocity is calculated.
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