When -multiple is selected, the generated XML files include not only the class they're named for, but also all previous classes that have been Javadocced in this run. If you're Javadoccing a large codebase, this could mean a 500K+ XML file, where only 1K or so is relevant to the class you're looking for. It also complicates automated processing of the XML files, since the generated XML files have a lot of information that just needs to be stripped out.
Looking at the code, it's because JELDoclet.save() performs an addNode to the same root element on every iteration, but there's no way to remove the nodes it has previously added. So it saves the file, but the root XML node still contains the previous class on the next iteration through the loop.
I've attached a patch for this issue. It adds a clear() method to XMLNode, clears the root node after saving the file, and re-adds the adminNode.
Patch to clear rootNode after each file save