I did a search and didn't see any other topics related to this issue in the forum (forgive me if I overlooked something). I am also having the same problem with my email icon and I'm not sure if it's related to the AWFUL software upgrade that was pushed on us or why this suddenly occurred.
The email in question is a POP account through GoDaddy. I've tried removing my email account, then went to App Manager > All > Email and cleared the data and the cache, also cleared the cache and data from BadgeProvider because I had read somewhere that this could help. Then I rebooted my phone and set up my account all over again, but when I synched everything, the notification icon only showed 99 emails when there were actually 100 in my inbox. Tried to mark them all as read, icon reads -1. Tried deleting all the emails from my inbox and then from my trash folder, still showing -1.
It's started to get really frustrating! Any way I can fix this? I really hope only alternative isn't to do yet ANOTHER factory reset because that's not even something I'm willing to consider.