clear all masks…i know you said you did, but do it again 
Also, transpose errors usually occur as a scaling issue. Check the preview window in the tool panel and see if you can see your entire mesh in that window. If you can’t (probably way too big) then use the deformations panel to decrease the size of the object (or use unify). Once the mesh is the right size it should transpose correctly.
If you have many subtools using the deformations one at a time can be tedious to say the least. You can get the plug in Transpose master to help with this. Hit the left/1st button (I don’t remember the name). Let it do its thing and then once you have one solid mesh, apply the unify deformation to that object. Then hit the right/2nd button to have the deformation applied to all of your subtools.
Hope that helps.