Conor, the links had been there for years. Obviously, I cannot say what my site is about etc, but if something is used that does not belong to us, then we link to the offical site of that person. These are low PR / grey bar pages anyway (in most cases).
The drop in PR hasn't affected SERPS nor visitors, but annoying that innocent sites get caught up in the mess.
The site is whitehat, professional looking, Gov IBLs, a number of homepage links from other sites (because they used things from my site) and were freely given by those people in return.
When PR6 I changed the ownership of the site (everything else remained the same). It remained a PR6 on the next update (it was only about a month later and I know the "snapshot" google takes is a few weeks proir to that).
But on the next update it went to PR4, and on the next update, a PR3 where it has remained as ever since. :(