My Nexus 7 was rooted when I was on 4.2.2. I accepted the 4.3 update and lost root, as expected. I am OK with running it as non-rooted. However, there seems to be some "left over" root file(s) somewhere. For example, when I start the Helium app, I receive the message in the attached screen shot. I can click OK and then run the app, but I would like to get rid of whatever is causing the message. I have tried doing a factory reset but the message is still there. Any thoughts?