Can you check if the emails are getting deleted off the server when you read them? If it does, it should reset the badge count.
For some reason they weren't deleted from the server, my iPhone POP account is set to delete from server When remove from Inbox, so everything looked fine, but I also remembered that it has been a couple of days that I have noticed that I was deleting the emails from that POP accounts on teh iPhone but then at night when getting home I still had the emails there, so obviously something was wrong.
So, I decided to delete the account from the app, this got rid of the badge, then I deleted the POP account from the iPhone and then created it again, then went to the app and added the POP again.
I can tell you that I have received about 4 emails from that acount and all of them has been deleted from the iPhone, from the server and the badge takes a little longer to update but it's resetting correctly now. So apparently it wasn't the APP at all, it was something on the iPhone that wasn't deleting the email from the server as it was doing and suddenly stopped doing.
So, for me it's working great now. Congrats.