@phaedrux I've made PID tuning and now everything is perfect. At least in static tests.
When I get the rest of the parts, I'll test it in print, but looks like for now all of my issues have been resolved. Thanks! 
BTW a lot has changed since I last configured the Duet machine (about 2-3 years ago).
The configuration has gotten much more complicated, but also very very powerful.
I love it!