@Aphrodite -- can you elaborate a bit?
Are all your messages marked read, and yet the unread count -- where, on the app's icon? -- show a non-zero number?
But you also wrote that you have older unread messages, so I'm probably missing something?
If you have unread messages, then they will be counted by Aqua, and will show in the app's main window (account list) and on the app's icon.
Is that what you're saying?
And you would like to see only the number of "actually new messages, just received now", is that it?