After importing my calibrated scene setup and then carefully setting up a T pose on a new bit of capture footage, sometimes the software thinks the model is about a foot lower than it actually is, and compensates by raising it up. Predictably, it then gets very confused!
You can see screenshots I took in this zipfile:
http://www.ian.chisholm.clara.net/pose_mismatch_bug.zipYou can see I lined the T-Pose up properly, and then I used the "Pose Mismatch" display to see why it kept going wrong. Oddly, the Pose Mismatch view thinks the model is about a foot lower than it actually is. Raising the arm of the model shows a green match further up (as shown by Bad Pose Matching.jpg).
I've experienced this a few times now, but it doesn't happen every time. It is always the same height differential as well.
However, if you make the T-pose, save the .mocap file, quit the software and then reopen it all, the mismatching goes away, so there is a workaround.