This happened on a few of my accounts – specifically the IMAP accounts on my Windows Mobile 6 device. Apparently this was a problem back with Windows Mobile 2003 but it seems to have resurfaced in Windows Mobile 6.
Even though all messages in an account are read; the “1 unread message” message still shows up on your Today screen. This happens when the internal unread message count becomes de-synced with the real message count. Instead of polling the server for unread messages, Windows Mobile keeps an internal database/registry key with this number. This problem also manifests itself in having “-1” unread messages or another off-count.
Luckily, it is pretty easy to fix. Download this program from freewareppc. Transfer and run the .exe from your device. It analyzes your accounts and fixes the internal database “unread” count.