Well majority of the problems are happening to the users on the local "Datacenter Exchange Server" which is in the same room as the BES server.
After talking to RIM TSupport they explained about the mail agents and some best practices and the recommendation of having BES users on a Exchange Server local. So I just want to concentrate on that connection.
Once I can stablize that connection then I can work on moving all BES user's mailboxes locally. Management will just have to deal with it or go without! :D
Mailbox issues are another story in itself. Prior management, administrators, policy's and buying three other global companies put Exchange boxes all over the place where they shouldn't be and don't' need to be. Lack of experience or something who knows...but they deemed 200+ users per site required a Exchange server. Myself and another new Exchange Admin are consolidating North America, Mexico and Canada. While we have our Euro and Asian Divisions working on consolidations too. We were at 50 Exchange servers worldwide when I started...and now less then 20! But still more then I want out there.