Hi netboss,
The bottom line is where the quadrature transitions occur. Each transition should occur at 25% intervals through the cycle. Deviations from those points would correspond to position measurement error and introduce "jitter" in the position measurement.which is more important, duty cycle or offset?
But I doubt if it would be a big problem. A perfect encoder would still have 25% jitter where there is no change for a while and then the position suddenly changes by 1 (quantization error). So your case might be similar to having a perfect encoder with half the resolution (slots). I don't think you mentioned how many slots you have.
The parameters for Threading have a Tau Parameter where you specify how much smoothing is made to the measured encoder position to reduce jitter. A normal value is 0.1 seconds. A larger value will reduce the effect of jitter but increase the time it takes to correct for a speed change.
HTH
Regards