Errrrh - I work with Bodyswap in version 1.2.0.10 regularly? It does have a problem detecting some of the morphs I use, which is annoying, but it does 'work'.
My 'workaround' is using bodyswap to default all the head-morphs on one model (for some reason, it never fails with headmorphs), manually defaulting all the morphs bodyswap missed on the other model, and then using VaM's built-in merge function to merge the two. Tedious, admittedly, but not intolerably so.
P.S.: I think that the problem could be some custom categories I made for some morphs a while ago (with the morphology external tool), and bodyswap not recognizing those categories because it operates off of a hardcoded list.