After installing 2003 server SP1 then 4.0 hotfix 3 the properties of the BES server in the manager changed from 4.0.4.5 to 4.0.0.0.. It seems like it went backwards..

If you stop all of your services and then start them up in the following order you should be fine:

Router
Dispatcher
Contoller
The rest of the services.

Thanks it worked