Hi Keith - the UVs that you get from MoI will be just the natural UV structure of the NURBS surface.
When your model is made up of multiple surfaces, these UVs are not really guaranteed to align together in any kind of special arrangement. I mean like the U axis of one surface may be lined up with the V axis of a nearby one, or they may be at a 45 degree angle to one another if you have trimmed-back areas of the model, etc...
If you need a particular UV organization different than that, you'll need to discard the automatic UVs that MoI puts out and then apply new ones using the UV mapping tools of your target program. I guess it sounds like you were doing that already, but yes that would be what is necessary if the built in UVs do not work for you.
I'm not quite sure if I understand the "inside out" UV problem really - I mean UVs give a mesh point a location in a 2D texture map - they don't point to an inside or outside of a volume like a normal does...
- Michael
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