1. The diamond/line separating the references from the remainder of the
document spans both columns when I would expect it to span one.
This seems to be true only for papers prepared for prl, not prb.
2. The "Electronic Addess" for the author appears in a footnote on the
second (last?) page, not the first.
I don't think this has anything to do with LyX, it's just how revtex
class behaves. You can see many examples of it on arXiv.
APS, if I remember correctly, uses some other software to produce
printed papers.
