Hi Ed,
It sounds from your description, like you have a UV mapping problem. I think what you need to do is import the obj file you export from the SeparateObj utility into another modeler that has a UV editor and edit the UV mesh (orientation and scale) to fit the kind of texture you intend to use in Hypershot. Then export that edited file to Hypershot and assign your texture. As soon as you start using textures that have a pattern or grain to them (things like wood textures or cloth patterns, for example) you'll need to start dealing with UV mapping to get the textures to fit correctly on many objects. Hope that helps?

Paul