Well, cridgit, I'm really on a roll with problem finding. Another issue I have is that if I adjust the Genesis pose with the Pose Controls on the Parameters tab, those modifications do not get undone by the PoseMaster pose transfer, regardless of  whether the "AutoZeroPose" is yes or no. The transferred pose is really messed up with arms all twisted and tangled through the body! Try zeroing Genesis pose and then using Pose Controls to move the arms down and forward. Then transfer a V4 pose to Genesis. Yikes!

I think the problem has something to do with the sign (+-) of the movements when transferred. If I go into the Genesis Pose Controls after transferring the pose and change the + to - and - to + on the used Pose Controls, things look better, if not quite right. This is kind of like the +- issues with the thumbs.

I look forward to your analysis of this issue. I don't understand how Pose Controls interact with posing with Bend, Twist, and Front-Back on the individual bones.