Ok guys. Let me first apologize. I was trying out 2 different things and ended up confusing them
1. Raspberry Pi running Stretch with INDI drivers installed
2.Raspberry Pi running Astroberry Unbutu Mate
The problem is on Stretch. With just the INDI drivers I can connect Kstars client to the pi INDI server. I can control the mount correctly, but joystick input stops the tracking.
This does not happen with Unbutu Mate Astroberry.
Some info that I hope is helpful.
After looking some more I noticed that in Indi control panel the driver info on Astroberry shows 0.3 and on Astropi3 it shows 0.4, for EQMod.
Astroberry does not strop tracking with joystick input. So this was working in 0.3.
One thing to notice is that there is backlash also in the RA axis so tracking might not be immediately visible after slewing east until all the gears come into contact again.