Hi Nicky,
I was able to reproduce this at my end. Until I get to the bottom of it, here's a work around for you, it will require running a few lines of code in the python editor.
#capture the current skin cluster, and write it to disk.
import zBuilder.builders.skinClusters as sc
sc_obj = sc.SkinCluster()
sc_obj.retrieve_from_scene()
sc_obj.write('C:/tmp/out_skin.zBuilder')
Now you'll need to open a new scene with your warped geometry and joints in it.
For this to work, there is no prefix. Just make sure the mesh and joints have exactly the same names.
#retrieve the skin cluster data from disk and apply to objects in the scene
import zBuilder.builders.skinClusters as sc
sc_obj = sc.SkinCluster()
sc_obj.retrieve_from_file( 'C:/tmp/out_skin.zBuilder' )
sc_obj.build()