I have the exact same problem with my Surface Pro 4 (among many many others that Microsoft refuses to fix). As a pro-tip you can disable the touchscreen in dev

I have the exact same problem with my Surface Pro 4 (among many many others that Microsoft refuses to fix). As a pro-tip you can disable the touchscreen in device manager. Even if you do this the pencil/pen will still work on the touchscreen, but 'touch' will be disabled, so you can can still use it in a pinch but without it being a non-starter device.