Re: Actually that didn't do it, just a one shot only fix.
Are we talking about Samsung TouchWiz counter, in the launcher, on the home screen, and on the app's icon?
Just making sure we're on the same page here.
Is the unread count properly displayed in AquaMail? That is, no unread messages, if I understood you correctly?
What if you create a widget instead? Does that get updated correctly?
Oh, and what's your phone's Android version? Since this is an undocumented function, it may not work very well on the older versions, say, prior to 4.3 or 4.4.