I've been waiting for MoI v4 to be released, so I can switch from Rhino v5. I can say that in Rhino v5, you have to flip the direction of the last profile curve (almost all the time). Rhino seldom gets the orientation right. The other problem Rhino has is it often doesn't have the same end points for the profiles. So you have to find a place that exists on all the profiles to re-orient the loft direction and location. So my suggestion would be try and see if one of the direction arrows has been flipped. Also check that each loft starts at the same point on the profiles.

Also, in Rhino v5, you can loft with a rail. That will help with the above issues. Not sure if MoI has a similar option.