I am also having the same problem. I've installed JNSQ through CKAN and when I install all of the dependencies alone (without JNSQ) mechjeb works perfectly fine. As soon as I install JNSQ, it breaks the positioning of the MJ window, breaks the settings window, etc. It's worth noting that MJ still.... works (as far as I can tell), it's just that everything defaults to the top left of the screen. Pretty much the error commented on in issue 1467 on the Mechjeb2 github. (I won't post a link so that this post will make it through moderation.)
If I then remove JNSQ, mechjeb is fixed. So the problem is DEFINITELY inside of JNSQ somewhere.
