Was the BB wiped before activating? Were there messages in the message list prior to activation? Was this for an existing user switching to a new bb?
Default setting for BES 4.0 message pre-pop is to forward headers only. You'll get duplicates on hh after activating when a backup of messages was restored to the HH before the activation. Full messages come from backup, headers only come from BES message pre-pop. Duplicates will not continue to be recieved on the handheld, but were placed on the handheld during the activation.