Thank you very much for the info. I suspected it, but couldn't be sure, as in console logs nothing showed up.I have the same problem. Hands Off! is the cause. v3.1.1 does not work with macOS 10.12.1. You can uninstall Hands Off! (and restart) until its updated to support macOS 10.12.1, or if you need Hands Off! then you can live with the problem, or revert back to 10.12.0 from a backup.
I also hoped so, so sad...I was hoping this update will fix the Intel HD4600 Graphic Issue with Safari but The problem still persist.