Is there any correlation between the position of the Roll Handle, and the invisible constraining sphere?
Yep. The base position of the bone is as you specify it in Bones. The bone will rotate such that, at ninety degrees of latitude, the bone will point in the same direction that the roll handle originally pointed (although, of course, the roll handle will move by then). Also, there is a bug (reported) in the program as regards moving roll handles (and bones generally) once you have already created an action or pose: When you move the bones, the pose will get screwed up on that bone and any effected descendants. The quick way to fix this is to go into the effected action or pose, delete the entire channel on that bone, and recreate it by hand. Not fun, but it works. If you’re having really wierd bone behaviour, this might be the cause of it.
