If you look in the Application Log, do you see any warnings referencing ConstructPIMFolder failed?
If so, search BlackBerry Technical Solution Center
for the error you find. There is a KB that fixes it.
Typically the Notes folder ID on Exchange changes and the BES no longer syncs that folder. To the BES it's the same as you deleting the Notes folder and creaing a new one. This does not work because the BES only syncs the default folders that are created with the mailbox.
I think you can run outlook.exe -resetfolder to correct the issue. If not the KB from RIM will at least prove it's the folder ID issue.