I was fed up with trying to find out the correct way to stop and start the Blackberry services. Here is the correct order and a script to do it.
net stop "BlackBerry Controller"
net stop "BlackBerry Dispatcher"
net stop "BlackBerry Router"
net stop "BAS-AS"
net stop "BAS-NCC"
net stop "BlackBerry Server Alert"
net stop "BBAttachServer"
net stop "BlackBerry MailStore Service"
net stop "BlackBerry MDS Connection Service"
net stop "BlackBerry Policy Service"
net stop "BlackBerry SyncServer"
net start "BlackBerry Router"
net start "BlackBerry Dispatcher"
net start "BlackBerry Controller"
net start "BAS-AS"
net start "BAS-NCC"
net start "BlackBerry Server Alert"
net start "BBAttachServer"
net start "BlackBerry MailStore Service"
net start "BlackBerry MDS Connection Service"
net start "BlackBerry Policy Service"
net start "BlackBerry SyncServer"