Not trying to hijack the thread, but I've got a similar question/issue. Love the app, and I'm now down to this last issue.
I've got Missed It! installed with Nova Launcher. All of my other notifications work (SMS, Touchdown, etc.), but I'm having a problem with Aqua Mail. It picks up new notifications okay, but it ALWAYS has at least a (1) showing after it checks the mail (regardless of my Missed It! settings (ie, Multiple events behaviour). Because all of the others are working fine, I'm guessing it's an Aqua Mail issue.
I've enabled notifications and clicked "only when new messages".
Under Smart Folder time period, I've clicked "only unread". There are no unread messages. (I've also clicked "use (Smart Folder) for notifications).
Any ideas?
As I say, I love the app (really well thought out) ... just trying to nail down this last pet peeve.
Thanks!