Having trouble with Maya Muscle. Created capsules don't follow joints.

I'm trying to make sense of Maya Muscle and am having trouble with converting the joints to capsules. When I do this, some of the capsules are pointing in strange directions and I don't know why. This is NOT a problem with the axis direction, I understand that. The capsule is maybe 10 degrees off. I also tried changing the joint orientations, but that did nothing.

http://i.imgur.com/tv2LpQK.png

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