You need to remove the Exchange manager from your BES server and install the application I installed two post prior. It replaces the exchange system manager for 2007.
BES controls 2003 via Exchange System Manager
BES controls 2007 via Colloboration and MAPI
The new API is necessary to get all the information out of the information store, thats most likely why you are only syncing emails.
Once you get it up and running just move them over.
Your best bet, is really to have two BES servers running, one for 2003 and one for 2007, if u need to make the swap without anyone noticing. Depends on how many calls your going to get. But the sync should work instantly once u get the new API installed. So they might not be able to send and receive for about 20 mins if you do it right.
I would, since I don't have the time to mess around is really just get the BES working for 2007 and migrate everyone over. 2003 is a piece of junk compared to 2007
Otherwise, like i said, update your bes to use Download details: Microsoft Exchange Server MAPI Client and Collaboration Data Objects 1.2.1
but make sure you remove the exchange 2003 componets first then restart.
you will need to hunt down the CDO.dll & MAPI.dlls if it exists and delete it after a restart so that the CDO and MAPI one is installed, they usually lurk in the system32 dir.
the 2007 exchange manager does not work with BES in a 2007 enviroment, I have already tried it.