Quote from OP:

"I tried editing another CR and made comparable changes (removing the :#) but there is no effect when conforming. They both use the same .obj. Does anyone have any idea what am I missing?"

Am I assuming correctly that you modified the CR2 to point to a different OBJ that you want to create an auto-conformer for? If so, the reason that the morphs don't work is they were created for a different OBJ. You would have to recreate all of the morphs to be compatible with the new piece of clothing because the morphs have to have the same geometry, polygon count, and vertex order as the clothing you are using.