With the updates I've been doing to the SMD Exporter, several bugs were introduced with skinned models.
Tonight I fixed most of them locally, including the problem of incorrect orientation and offset in bodygroups. I still have a couple more things to clear up. I expect this update to be out this weekend, and I think it will deal with all the problems that were introduced since the 1.856 update.
Look for the update soon.
To my knowledge, all problems relating to this have now been rectified in WWMT 1.861 (and SMD Exporter 1.33).