Settings has a notification cant make it get away?

Can you provide a little more detail?

I'll bet it's a notification for the update to the just-released iOS 6.1...Go to Settings/General/Software Update and you'll probably see a message stating that iOS 6.1 is ready to be installed. The only way to get it to go away (AFAIK) is to update your device.

settings>general>reset>reset all settings

Try a reset: Simultaneously hold down the Home and On buttons until the iPad shuts down. Ignore the off slider if it appears. Once shut down is complete, if it doesn't restart on it own, turn the iPad back on using the On button. In some cases it also helps to double click the Home button and close all apps from the tray before doing the reset.

Try to reset the device (won't delete anything like music, apps settings, etc):

Press and hold the Sleep/Wake button and the Home button together for at least ten seconds, until the Apple logo appears.

Also try logging out of your AppleID/iTunes account, then log back in. Seems like the update is not being flagged by your AppleID as being actually applied, even though you said you already applied it. What does Settings/General/Software Update tell you? If you've updated correctly, it should say "iOS 6.1 Your software is up to date".

When I updated to iOS 6.1 (from 6.0.1), I did it through iTunes (did not use the OTA option even though it had already downloaded to the devices) on all my devices and had no trouble with the notification clearing. Maybe it will sort itself out in time...this is the first I've heard of the notification not clearing after updating.

I have the exact same issue on my iPad. Nothing seems to clear it.