Give this a read: Managing BES <> Exchange Mappings - Port3101.org : Your BES Connection

I'd recommend giving this a try. Make sure no Exchange server is talking to both BlackBerry Enterprise Servers ... isolate users from a given mailbox server to a given BES. This'll help minimize the load on a given Messaging Agent.

Then, move users to other Exchange servers if you can, further isolating ... The last thing you should then do is implement the NumAgents registry key as it'll help ... but make sure you have enough resources on the BES.