1 - They are emptying their Deleted Items before the BES does it reconcile scan
2 - They aren't waiting long enough, as the reconcile process only runs once every 20 minutes
Depending on which version of BES you are running (Exchange, Notes, Groupwise), it could be a few more things (atleast I know of an issue for Exchange).
In the beginning the Universe was created. This has made a lot of people very angry and is widely regarded as a bad move.