It works for me, what units exactly do you use? e.g. when I used human and footman, footman couldn't build, he just started the building (because he hadn't the Repair ability).
There seems to be some problem with races: while transforming the race of the base unit is used. Orc builders can't build human buildings and other way.
When i transformed peasant to peon, he couldn't build orc buildings, only human (which i added to him, 'course)
Hope my study helped, if you describe exactly what you need, i can look into it further.