Ok; the files mentioned in this issue can neither be found here, nor on sourceforge. I made a little test, overlaying the header.pdf with letter.pdf and a second test overlaying letter.pdf with header.pdf.
Overlay head = new Overlay();
PDDocument resulthl = head.overlay(header, letter);
PDDocument resultlh = head.overlay(letter, header);
The result in the overlayl-h.pdf is, what I expected it to be; the result of overlayh-l.pdf is not what I expected it to be, but understandable. I'm not sure if this is the default-behaviour or really a bug. Perhaps someone can take a look on it and revalidate my result. To me this bug is "Not a Bug".