Also having this issue and nothing from what is mentioned here helped. Tried portable, tried jre 1.6, tried sh3d version 3.4, tried disabling java3d by env. variable (now causing directX/opengl error at start up).
Issue starts right away when any tooltip appears, then it feels like re-paint is totally messed up (almost like double buffer content is painted where your mouse is).
Found also other SW with similar reports: https://github.com/chatty/chatty/issues/69

My setup is Win10, 64-bit, Asus G752, Nvidia GTX1070, factory drivers