Help Persistent indicators on read SMS, E-mail, Facebook, and other notifications

[element6]

Carrier: Verizon
ROM: Stock I535VRBMF1 - Rooted, ODEX
Radio: VRLF2 applied after ROM (latest OTA is horrible for me)

Recently returned to stock ROM after being on Paranoid Android for at least 1.5 years.I've got everything sorted out but this annoyance. I've been hunting for a fix for a good hour and trying stuff but nothing seems to work.

Problem:

• SMS are received and read, but the "1" over the SMS icon on the home screen never goes away except after a restart or if I delete the thread. As soon as I receive another message after it has rebooted, the 1 returns, even if the phone is on and focused on the SMS thread during the time it receives the SMS.
• SMS notifications don't disappear from the pull down bar even after the message was read.
• Facebook notifications don't disappear from the pull down bar after I go on the Facebook app on the phone and look at whatever it was notifying me of. Additionally, the Facebook chat app typically leaves an unread message indicator over the bubble icon (on the homescreen) of a friend I was talking to on FB chat no matter how many times I look at it. It usually doesn't go away unless I drag the FB chat bubble to the X on the homescreen to get rid of it.
• E-mail notifications for both Outlook and G-mail do not disappear from the pull down bar after they have been read, even if the message is deleted. I have to hit clear for everything all the time.

I have tried this without success:

• Settings> Developer Options> "Do not keep activities" = unchecked. It was never checked to begin with. I checked it, rebooted the phone. Same problem. Unchecked it, rebooted the phone - same problem.
• Settings > Application Manager > All applications (tab up top) > "BadgeProvider" app, "Clear Data". Restarted phone immediately afterwords. No change - same problem.

Any ideas?