Don't know if issue or resolution is related, but we had this issue related to device blocking emails. The BES would send the email and receive delivery confirmation, but the email won't show on the device. Same results with <confirm> messages.

Goto below on device and look for blocked messages in RED:

On Device ---> Settings > Options > Security Options > Firewall


We found that Incorrect Encryption key blocked some messages and was resolved by doing the below :

On Device ---> Settings > Options > Security Options > General Setting (or Information) --> Click on the line Desktop.... --> Regenerate Encryption Key.