Very weird issues with the paint tool:
Open Paint.Net Move Mouse
Also, by print screening the above and pressing Shift+Ctrl+V, this happened:
Also, after zooming in and using the Pencil tool the whole canvas seems to draw a different zoom level for a split second then reverts to the correct zoom then repeats.
[EDIT] Disabling hardware acceleration fixed the issue, not sure why though! Let me know if there's anything I can do to help you debug this! [/EDIT]