That's right, because of the bad parsing (let's not go into it again), I exported the individual animations separately. If not automatically reading all your animationLinks, what about something like Skeleton.addAnimation(String xmlFile)?
So to explain the initial problem: say I had two animations, a walk and a run. The model was being loaded such that the end of "walk" was the beginning of "run." It must come from bad parsing, as the animations had the right number of frames in the skeleton.xml file, so I split them into separate xml files. Which brings us to this current problem, whereby the loader doesn't load the animationLink references in the main skeleton.xml.