from personal experience I can relate the following info for each points:
1. If there is a main + backup server, this problem can arise when the main server is down and the blackberry starts routing through the backup server. Just yesterday, we had a problem at our company with people experiencing calendar sync delays of up to 5+ minutes and the only thing we could find as a cause was that the mail server those users were on was down, and their info was being routed to the backup mail server.
2. This problem seems to be an issue with the state database on the BES, from what I've experienced. Recreate the state database, and emails start reconciling properly again.
Ghetto stats: bberry 8130 :: desktop manager 22.214.171.124 :: handheld 126.96.36.199 :: Lotus Notes 7.02 :: BES 4.1?