When you have an IMAP Gmail account and you have labels assigned to incoming messages then a message is counted double, one time as incoming message and one time as new messsage for that label (when you have more labels assigned, then it adds up).
The result is that you have a new message count of for example 6 on your status bar, while the real number of new messages is 3.
Would like to see that Aqua mail would take labels into account.
Thanks, I really like aqua mail, it's a fresh look on email clients and has lots of features.