I'm still seeing this problem where the pencil, text, and highlight annotations all fail to work when XInput is enabled. It may have something to do with VirtualBox. I see it on 2 VMs, one running Jessie and one running Stretch, but I don't see it on my baremetal Jessie system.
I have tried uninstalling the VirtualBox X11 guest additions, but that didn't seem to help. When I get some time, I plan to track down some other applications that use XInput and see if they show similar problems. regards, mike