Thank you Microsoft support
If anyone out there has ever tried to justify to management the cost of a TechNet subscription then the 2 free support calls that you get more than cover it. They have dug out my new Exchange 2007 server which was queueing email bot inbound and outbound and not putting it in users mailboxes. It turns out that the version of Exchange 2007 I installed (complete with SP1) had config files incompatible with the version version of .Net I had. The guy re-wrote all of the Exchange services config files and now everything is fine :) There is no way on this Earth that I would have been able to track down that problem.
So its a big thank you to them (who have saved my life many times over the years), and a damned good reason to get TechNet if you don't already have it.