So dome is actually always factored in in Align module but it was more complex than that and has to do with using motion WE/NS controls which don't cause trigger in the dome. I submitted preliminary change to INDI for this which I hope gets to fix this, but we'll see tomorrow.
Ok Jasem i've done all that, including flashing a new Sandisk micro sd card and adding in any updates via the updater and I have run an hour long test to see if there is any issue remaining. Guardedly; because I've thought previously that the problems had been solved with other solutions; there were no issues that showed up this time. This was an indoor test with a fully loaded mount, but I shall have to wait for a few days before I can test the same setup on real stars.
My question now is, why, on what has been a closed system, ie not connected to the Internet, do problems like this arise that seem only to be fixed by a software upgrade? After all if there is no input from the WWW then all the bits should keep on doing what they do with no problems. Do sd cards wear out? if so why? I have used a 32 Gb Sandisk card for this so did not expect there to be a problem. What other issues can arise?
Thanks for the input.
Skywatcher Explorer 200p on HEQ5 pro
Rpi 3B running Stellarmate.
Canon EOS 550D
Recently I have faced exactly same issue using my Astroberry with Kstars/Ekos.
I have figured out that the axis had been inverted by me in the Mount Control window before, so uncheck of that chekbox helped me to fix it.