Before loosing my mind I have in the last hours making some other testing and found out some important details on one of the problems, so here's what I found;
First, there are two distinct problems
1 - Frame dimensions - this one has to be solved on the driver / sdk our using ekos / indi panel workaround . So this one stands the same situation as before.
2 - Frame loop hanging:
Now for this one I tried to isolate the problem, without using KStars/Ekos. So I tried using CCDCiel and PHD2 connecting to the latest drivers/sdk and.... voila!!!!
No problems at all stopping the frame loop. I even change binning during capture and still no problems. No matter what I do the camera stays rock solid without hanging.
And there is one important detail I found.
In both applications when I manually stop the loop, the last frame is always downloaded after the stop. That is not happening in Ekos. As soon as you stop the loop, the camera
immediattly hangs, so it seems that the QHY6 does like interrupting the frame download. I remember this also happened to my Atik 420m some time ago and it was corrected
after an update.
Soooooo...... it seems this only happens in ekos. I hope this helps troubleshoot at least one problem.