I consulted for an environment that had a really slow delivery for email to the handhelds which took about 15 minutes to an hour. I tried all the standard tricks, which all failed. Finally broke down and engaged RIM and they suggested that I apply the following patches to all windows 2008 R2 servers that are used in email flow. This would be the BES server, AD, and Exchange servers.
http://support.microsoft.com/kb/2155311
http://support.microsoft.com/kb/979149
Once I did this, handhelds started to operate as they should! I think it is a combination of the patches and the other things that I did (moved BES to a SQL server, increased agents, so on) but problem solved! Go figure….