Messages not showing up

I just started experiencing this problem yesterday after no issues since I have gotten the phone. I have to gmail accounts essentially, even though one is a university email address, however it is run by google. Basically the past few days I will get emails from the one account fine. The school account will now buzz that I have a new email, but sometimes it won't show up that email account folder, it will only be in the messages folder. Sometimes it does go to the email account folder, yet it doesnt have the star on it that i have a new message. it only does it for the messages folder. I want to keep my things seperated, so does anyone know what could be up. I resent service books and did a battery pull already to no avail. Even deleted the account and set it back up.

This is still happening and I can't find any info about it. This is my first BB so I don't know all the OS tricks. Anyone have some info?

This is probably a long shot but you might try this. Go into messages and click the blackberry button (to the left of trackball). Click on option, general options and scroll down to SMS and email inboxes. If you want to keep everything separate in needs to be set to separate. Save and then see if that works.

it was already set at separate so that isn't it unfortunately.