Actually it just noticed a mistake in my setup: nDisplay only supports one camera that looks in different positions. While this approach might look correct at first, it is not actually two cameras looking in the same direction, being eye_distance centimeter apart, but rather the same camera just pointing a slightly different direction.
It is as far as I know only possible to achieve the stereoscopic effect using the nDisplay Launcher, which is a problem for your and my situation. So if anyone has a solution to this problem, please let us know 