erm, well I would have suggested blender, but you jsut excluded that. TBH I think that you have to know the right way of unwrapping with programs like blender. For instance: sometimes you have to select certain faces of a model and unwrap using the "project from view function" to get the shape to not deform, and then pin a lot. But, to me, it sounds as though you're model has two verticies in the same spot, correct? If that's the case, with blender you could just select the entire model and hit control+w and then click the "Remove doubles" option. This pretty much fixes your problem how you described it. Best of luck!
