Browser --) Alerts if you get a browser message (like push weather)
Level 1 Messages --) A message identifed as Level 1 (important)
Messages --) Email
MMS --) Multi Media Message (like SMS but will have sound, images ect..)
You should be able to go into your BIS setup and setup filters to send predefined emails to your BB as level 1. I have pins as level 1 (setup in the BB) and then in BIS sI have a filter that says for all messages from my wife to send as level 1. You can set a different tone on the BB for level 1 messages and in 4.2 OS (which will be out soon for the 8700) they appear in red in the message list.
Have you installed any programs that notify you of emails, calls, things like that? You could have two different notifications going off from the two different applications: the notification from the OS and another program. Just a thought.