@jpaana Thanks for answering, I have not thought to that case. I don't know the precision you get when using a high quality mount in a fixed observatory and how alignment may still be relevant in such a case.
@vineyard The mount driver does not have a 'meridian flip' command. It only offers track, slew and goto (and sync, guide). When tracking or slewing, it runs as long as it is told to run, even if it crosses the meridian (it may stop if you have set/enable limits).
You may make three turns in RA if you like. Concerning gotos, it always performs a goto with counterweight down at the given target (unless it is told to do counterweight up, there is a property switch you may set before issuing your goto).
That way, client/user may image passing the meridian without performing a flip if its setup allows it. Or it may start a session east of meridian without performing a flip if it starts counterweight up.
You have nothing to fix in your case. If you repeat your last test (start tracking east of meridian counterweight down, no alignment), just wait the target pass the meridian, then manually issue a goto in kstars to the same target, the mount should flip.
As I previously said, the problem seems to be that the client (Ekos) is using celestial coordinate to issue the goto performing the flip. It should use the true telescope coordinate, or wait for the side of pier property to toggle (the driver uses true telescope coordinate to compute this value, unless someone changed that).