Followup to comment #17: when I run apt-ftparchive on a mirror server running Ubuntu 14.04, I do not have the same problem. So some change between Ubuntu 12.04 and 14.04 fixed the problem I was having.
Followup to comment #17: when I run apt-ftparchive on a mirror server running Ubuntu 14.04, I do not have the same problem. So some change between Ubuntu 12.04 and 14.04 fixed the problem I was having.