Mount’s with hi-res encoders on the DEC axis fight with autoguide pulses if the autoguide commands cons too frequently.  In EKOS, I use very long guide exposures to help prevent this conflict, but this is not ideal.  PHD2 has a camera delay, that I can set to 3 seconds, which improves guiding on my EC2 mount.  Separating the guide exposures length from the guide pulse frequency seems to be a good idea.

You can perhaps increase the minimum duration pulse in the settings?

It's not an issue of pulse length, but pulse frequency. Once a pulse is sent to the mount, the internal mount encoders will react, and the guider needs to wait for the encoders to settle down. That can take several seconds. Otherwise, the auto guide software sees the encoder reaction as more error, and keeps sending pulses. This creates an oscillation that is difficult to control.

By increasing the exposure length, I can avoid the encoder fight, but these longer exposures are not as effective to bring the total RMS down below 0.4 arc seconds. In PHD2, with the camera delay function, I can use shorter guide exposures, along with lower pulse lengths, and get much tighter guiding. Most people never use the camera delay, or even know it exists. But with dual encoders it's the only way to get great guiding. We just need to have the ability to pause the guider for a few seconds after it issues a guide pulse. PHD2 calls it "camera time delay".