The description you provided of the network environment implies that your second BES server has to make MAPI connections to remote mailbox servers. The minimum latency as recommended by RIM is <35ms between the BES and Exchange servers. It is also recommended that the BES and Exchange servers reside on the same LAN to facilitate that minimum requirement. But we all know that isn't the case in most organizations.
What you can try to do to lessen the issue is possibly reduce the polling interval between the second BES and the remote Exchange servers that it "speaks" to.
Also have a look at the MAGT, SYNC, ROUT and DISP logs for the second BES server and look for "packets" or "response" not received from devices that's assigned to those 40+ users.
You could also try sending a "ping" test (using "confirm" in the subject line) to those devices to determine the round-trip time.