Steve, I have been turning off in-sequence checks because I was trying to avoid re-focusing as I have a problem with that, but you are right I had verify capture set to 0 frames and a large re-set pipeline value of 30 mins. From what you say the answer to my question is: Set the EKOS Alignment values so Alignment module is called after a period of cloud otherwise guiding continues at current location which may have drifted away from target location.

Should I set verify frames to 1 so it checks immediately and set the image delta to 0.3 as I usually set my-realign accuracy to 20 secs?

There is an underlying issue where the mount goes walkies (star trails) when guiding is suspended. This doesn't happen every time but quite often. The drift each time is different lengths and different directions but the pattern is always the same as below. Dots and lines in one direction.

This could be because my mount has developed a fault so will check that out on next clear night taking a long exposure un-guided.
What does "re-set pipeline" actually mean?