Jasem you're right, at startup iOptron driver overrides MF setting in HC, it happens to me too. Fix is setting it in the driver and saving configuration, as you said.
Euripides, you have to let the mount track some time AFTER CROSSING MERIDIAN, otherwise MF is not going to happen. In iOptron at "Meridian Behaviour" setting "Flip" or "Stop" doesn't matter here, since MF will be triggered by Ekos; but the "Limit" you set does matter. Basic rule is:
0 < EKOS LIMIT < MOUNT LIMIT
Example: set Ekos to trigger MF 3° after crossing the meridian, and set mount limit to 6° after crossing meridian.
Ekos limit should be greater than 0, because Ekos and mount must exactly agree on which side on the meridian we are: allowing to track some degree after crossing it, relaxes the precision needed and accounts for small difference in models and approximations between Ekos and mount firmware. Mount limit should be greater then Ekos limit, because some time is usually needed to complete the running capture when filp time occurs (should be: MOUNT LIMIT - EKOS LIMIT > LONGEST EXPOSURE PLANNED).
And MOUNT LIMIT should be small enough to avoid the mount smashing your equipment on a tripod leg or something).
As we speak, I remotely logged in to my setup and just pressed "Tracking on" to let the mount free to track. After a few minutes when I check back, the mount was idle. (My mount is parked vertically, ready to PA)
Is the "Meridian Behavior" tab in iOptron drivers new? I had the same issue appear (drove me nuts for a few nights before I noticed that tab). I recently installed 3.6.9 from scratch on an Ubuntu mini-pc, so it is possible that I had correctly set those values in my CEM25p driver nearly two years ago when I first installed astroberry on the pi, and the correct settings persisted when I switched to a CEM40 in December. But I have absolutely zero memory of ever visiting a meridian tab in the driver before.