Hi Daniel, I'd recommend trying the V4 beta version which you can get from here: http://moi3d.com/beta.htm .

It has various improvements to STEP file import, one of which is some fixes to instance positioning bugs.

For the "scrambled mess" problem that could be a problem with Maya not liking complex n-gons. Try using the option for "Output: Quads & Triangles" when you export out from MoI rather than "Output: N-gons" and see if that is not scrambled. If that doesn't solve it can you please send me a file where you're having this problem, you can e-mail it to me at moi@moi3d.com

- Michael