I noticed that this very topic (the default file descriptor limit) is
currently being discussed on the ubuntu-dev mailing list.

In particular, there was a little discussion of the fact that 
/etc/security/limits.conf does not apply to services:
  https://lists.ubuntu.com/archives/ubuntu-devel/2010-September/031493.html

The thread also covers various situation where otther applications are
hitting the limit; if you (Alex) are lucky perhaps something there will
give you an idea why you are doing so but other sites don't seem to
be....

Nathan

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slapd Too many open files
https://bugs.launchpad.net/bugs/632314
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