First of all, let me say I really do like Aqua Mail. So much so that I purchased the pro version.
My problem is simple. I have new message notifications enabled. When I receive an email in either of my two accounts, the notification shows up, etc. I can go to the inbox and read the messages, delete as necessary, etc. When I do that and return to the home screen of my Samsung S3, I get another notification, telling me I have more new messages, which are the same messages that remain in the inbox after I am finished. I should note that I do not mark them read on the phone, but wait until I am on Thunderbird on my home computer. Throughout the day, I will continually receive notification of those same messages, even though they are not new.
I am not complaining, but I am to the point that I am about to disable notifications completely. Surely, there is a way to stop this from happening.