“so I have 3,000 mailboxes in a single, multi domain forest. When I go to recipient configuration I only see a subset of them all? What gives Chad?”
By design the exchange management console only shows recipients from the currently connected to domain. To change this you need to change the scope of the filter. This allows you to change and see the entire forest contents or just another domain.
Don’t forget though there is a default limit to the number of items displayed for that filter set. Out of the box this is 1,000 objects. This too is customizable but it may affect performance.