Encoder on 7i96

I am hoping you can help me out. It looks like my signals, A,B and index from the encoder are coming in correctly, but my velocity is not right at all. I attached a picture of the halscope with the inputs and the velocity.

Can I fix this in the pncconf?, or do I have to edit the HAL settings in the file? From what I can tell I have something kind of off, but no idea what.

The velocity looks OK, the variation is due to quadrature error.
(that causes a difference in time between edges even at a constant speed)
this will diminish at higher speeds with high resolution encoders
(or if you can adjust your encoder phasing and symmetry).

If the velocity is for an on-screen display, you can low pass filter it.

I want to be able to set it up to do threading with it, I am on my first steps, getting the signals back to the board right is a win for me.