Even after deleting the history and freezing the transforms it is still behaving the same when I use Unforld3D. Here is a screen shot of the layout settings. I've pretty much fiddled with everything in there without success. Do you see anything I have set that might be causing it not to work correctly?
I've never had much luck using Layout to set correct scaling when the pieces aren't matching. We do have a get/set texel density under the UV Toolkit's Transform header. I usually use this before doing layout, picking a 'good' face to set the others.