mechjeb function on rotated craft?

[Sprool]

I was playing with mechjeb on a hab pod, made of 3 cylinders turned through 90 degrees to make a horizontal tube - added legs and rockets, then turned it back vertical to launch but the mechjeb control box on the pod decided it wanted the pod+lifter to fly horizontal and not vertical into orbit. Is there a setting so you can change orientation or does mechjeb not function properly if you use a rotated or inverted part to attach onto?

[Starwaster]

The orientation of the part you are controlling the craft from determines which way MJ2 thinks is up. If MJ2 is trying to fly horizontally then that means the controlling part is currently oriented horizontally. If you didn't manually try to select a part to control from then it's the root part, the first one you placed.

[Kerba Fett]

I've run into issues with non symmetrical ships not knowing which way is up. The navball would sometimes be at a 20' angle when sitting on the launch pad like it's affected by the COM. The easy fix was to select a docking port on top of the ship and select "control from here"

Your marker should be centered on the top of the blue half of the navball before attempting takeoff.