As per my previous post I was considering attempting an upgrade to Sharepoint Foundation to hopefully fix my problem. But you cannot proceed with an upgrade until your WSS3.0 site is healthy.
But here is a great article from Andy Phelps.
This article is really simple and quick to follow and works a treat. Although I would imagine SBS2008R2 will include Exchnage 2007 SP3 & Sharepoint Foundation and a nice installer that does it all for us :) But we will have to wait and see.