The ImageReference problem is related to an name change in the internal classes used by the C# code -- but it shouldn't occur as long as you take all the classes in the LeapC folder from the same branch (i.e. they should be internally consistent, but not necessarily across branches).
On the twisted thumb issue, we use a script (TestHandFactory) that sets the hand properties for the default pose. The thumb's up vector had the wrong sign on its z component. It wasn't noticeable in capsule hands, but caused this issue in rigged hands. We found the problem last night; I don't know if the fix has been checked in yet.