Running BES 4.1 (SP3) on MS Win 2k3/Exchange 2k3.

Device is a PEARL. Had to do a re-activation (wipe) now after the activation no messages appear in the inbox.

Pre-population settings on BES are / 14 days, 500 messages

Any suggestions?

I beleive if you don't remove user from BES prior to new re-activation it wil not re-populate messages as those were already marked in user mailbox as forwarded already. If you remove it click yes to clear blackberry information from user mailbox. re-add him and clear stats as well. reactivate after that. That should then prepopulate emails as configured 14/500 whatever is met first.
Hope it helps.

ya pre population works if another PIN is recognized, by removing the user and user stats this removes the PIN, if you have a replacement device you shouldn't need to remove and re-add as the BES will recognize its a new PIN and pre pop.