(1) Workaround (involves the user)
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Kinda silly but innovative.
Article Title: Separate BlackBerry Enterprise Server email messages from BlackBerry Internet Service email messages on the BlackBerry device
Article Number: KB12938
Link: View Document
(2) Create a seperate icon for BES messages
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Requires running a SQL script to turn on the flag for display of the icon.
Article Title: How to create a separate icon on the BlackBerry smartphone for BlackBerry Enterprise Server messages only
Article Number: KB15003
Link: View Document