So after many discussions with Rogers BES Support, they basically suggested I do a knife-edge cutover and see if the problem persists.
Two days before the outage, we had to cut over our Exchange 07 Cluster from the Active to the Passive, reboot the Active, cut back and reboot the passive.
The next day all of the users on the troubled BES reported that their Blackberries suddenly worked great.
I just closed the ticket with the support. They didn't have any explanation for it. Lesson learned for next time though, if there are unexplainable problems on the BES, try rebooting Exchange :P
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