This tutorial? I haven't followed it through fully, but it seems that his OBJ mesh has material zones defined, not groups, and he's using LithUnwrap to convert one to the other. You're defining your groups in Cinema, which I don't use, but I think you'll find that its OBJ export is unreliable. Get Spanki's Riptide plug-in from here if you don't already have it. The background section on that page should tell you all you need to know about why not to trust Cinema's OBJ export. Cinema's hierarchy will be ignored whatever you do, since that information isn't carried by the OBJ file. Once we're sure you have a meaningful OBJ mesh, with the right groups called the right thing, we can take it from there. If PHI Builder is mixing up the group order, then it's just a case of dragging them back into the right positions when you assemble the hierarchy. That's all I can think of for now - over to you...