I have a blackberry 9700, and I have 171 emails according to my little icon. When I go into the email folder, it says sms messages up at the top, and shows zero messages in the folder. My sms and email have always been separate.
Have you checked your messages options? Go into the messages folder, press menu, then options, general options. What does it say under SMS and Email Inboxes? If it says theme controlled, what theme are you using? To determine your current theme, from your home screen, press menu twice, then go to options, then click on Theme options.