The shoulder is probably the most difficult part of the body to rig, and I haven't really succeed with neither of the MH rigs. There also seems to be a problem with the elbows bending in the wrong direction, presumably because the upper arms are twisted.
There could also be some problem with retargeting. Can you specify the bvh file (e.g. CMU number), and I can have a look. If nothing else it can be used as a benchmark for shoulder and arm rigs.