I have this problem too: In ON 2016, when I write anything with the pen, it draws on the screen and then at most a second later, it disappears. I have handwriting recognition disabled. I am currently on:
Windows 10 Pro, version 1607
OS build 14393.447
i5-63000U CPU
8GB
64 Bit OS
Surface Pro 4.
But I doubt that info is relevant, as I had the same problem on a Surface Pro 3 last year. I brought it into an MS Store, and they had me wipe and reinstall the OS twice before they gave up and actually gave me a new computer. I installed Office 2016 on
it and had exactly the same problem. I uninstalled it and went back to 2013.
The version of ON 2016 I have now is:
1610 (build 7466.2038)
I really thought this nasty bug would have been fixed by now...