I have a note 3 and galaxy gear. After updating to kitkat I have this problem with the phone constantly notifying me of new emails, even though I have already acknowledged the email. Prior to updating, I was able to swipe the new email notification and It would not renotify me until a new email was received, now after about every 15 mins I get a notification to my phone and my gear saying there is a new email even though its the same email as before.
The only way to stop my phone from renotifying me is to delete the email completely. I have ensured that Gmail notifactions are off, and am only using the email samsung app.
This was working fine before but now I am going crazy and not even wearing my watch because it is so damn annoying.