When EKOS finds a too high HFR during a sequence it starts an autofocus run. That one suspends guiding (good thing) and re-enables it once its done. The guider then oftn has to do larger corrections in the first seconds and has large deviations.
So I had specified a guiding settle of 5s after a resume in the Capture options of EKOS. While this seems to work after a dither, it is ignored after an autofocus, the capture immediately continues as soon as AF is done, so often the first frame after AF gets bad