I've made two more test and at the same height... about 7k become uncontrollable. http://imgur.com/a/CkKdF
Looks like that I've been able to fix it by dismounting all structs and then reinstalling 'em
This is pretty irritating, btw, I'm open to every advice on this kind of problem 'cause I would like to take in orbit some weird hardware, so Tips are always welcome
Look how far it goes without pushing a single key http://imgur.com/27jH1MS
MaximilianPs's post in Multi Docking Port help was marked as the answer