I am having trouble with the tutorial "Introduction to Motion Capture in MotionBuilder". When I put the bvh file onto the story window, the skeleton is all skewed up and contorted strangely. Is this an issue with the new version of MotionBuilder? Is it a bug? fix and or workaround?
That's interesting. It does look like something happened in the later versions of MotionBuilder to affect those particular BVH files. You should be able to find other free BVH files on the web as there are quite a few sites out there that offer them. For example: Mixamo has some free ones as well as the Ohio State University Motion Capture Lab has a few various BVH files available for free.
Just keep in mind that some of those other files may not match up with the t-pose rig in the Introduction to Motion Capture in MotionBuilder as there aren't the same number of joints in the BVH files as the control rig. If you don't want to mess with those, I'd recommend checking out the Introduction to MotionBuilder 2012 tutorial. Not only is it newer, but when it covers using motion capture data the project files use MotionBuilder's native FBX format to help eliminate interpretation errors like the one you've come across. Hope that helps!