Look in Nookcolor tools
if its checked, uncheck it, recheck it, reboot...
Good catch, been a while since I was on stock rooted....and by a while I mean a week
OP, Do what Darmeen said first before you try any other fanciness or app shenanigans.
Follow along with the video below to see how to install our site as a web app on your home screen.
Note: This feature may not be available in some browsers.
Look in Nookcolor tools
if its checked, uncheck it, recheck it, reboot...