I feel your pain (or at least your publisher's pain)...
Here's my take on what's probably happened:
either (1) the site got penalized. or (2) the site fell into the supplemental index (e.g. google hell). search for "supplemental index" or "supplemental results" and you'll find plenty of info.
For (1), it would likely be for paid back links, a link exchange program, or too many incoming links coming from "bad" sites (e.g. directories that require a sign-up where google thinks they should penalize those who signed up.
I would say that if you don't have paid backlinks, 1 is very unlikely.
More likely the site went into supplementals (2). This can be caused by a lot of things but the #1 issue is link relevancy and value. 1 link from a PR4 site is worth 100s from unranked (PR0) or directory sites. Get a PR5-9 to link to you and you'll probably rip the site immediately out of supplementals and back into the main index.
You can determine which pages are in the supplemental index by doing this:
site:www.yoursite.com/* <- these results are in the main index.
then search for:
site:www.yoursite.com/ <- these include supplementals
if your main site isn't in the first listing, your entire site is in supplementals.