Why does iMessage continue to make sounds and display banners on my Macbook Pro (Retina) even though I have removed it from my notification center?

I hate that my messages pop up while I'm watching Netflix, and I have finally removed Messages from my notification center. Yet, for some reason i still keep hearing the noise that lets me know I have a message, and I a still seeing badges pop up on my screen every time a new message comes in? What's the deal?

I talked to Apple Support and we at least stopped the bleeding, a little bit. These are the troubleshooting steps I did before I contacted Apple Support:
1. Reinstalled OSX
2. Restore the last known good Time Machine Backup.
This did not fix my issue, so I called Apple Support and they told me this:
1. Turn Power off.
2. Wait 15 seconds.
3. Plug in Magsafe adapter.
4. Wait 15 seconds.
5. Hold down the Shift+Option+Power Button for 20-30 seconds.
6. Turn Power back on.
Ok, this stopped the bleeding a little, but as soon as I plugged in a Apple USB Superdrive
and a Apple Mini Displayport to VGA Adapter. This "USB Devices Disabled" pop-up pops up like every 30 minutes now. At least, it is not constantly popping up after I close it, so I guess it will do for the temporary. Going to contact Apple support, later, though to see what else can be done.

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