Sorry, I have not been able to look at these properly until today. rickyinmotion, in your scene, I see what I described above -- that instances of MXS references can render incorrectly. This is the same issue we are currently working on; here, for example, are two versions of your scene rendered, where the left uses two MXS references, and the right uses one MXS reference, and one instance of that reference:
AlexP, either I do not understand the problem, or my test is set up differently than yours, but I do not observe any 90° rotation when I make a reference of the MXS you sent: