This issue is probably best described with a video. Here is a link that should make the issue pretty clear.
https://www.youtube.com/watch?v=ktQwVLGzfXQ [2:50]

To explain what's happening in the video: I have a Cintiq 13HD tablet which plugs into my laptop through HDMI. GIMP will trace the cursor fine using the tablet pen with just the tablet on. When a second screen is added, there is an offset. This exists only with the pen, not the mouse.

The Wacom pen and eraser are set as "Screen" in the Input devices. Changing to "Window" also offsets, but at a different distance. Changing to "Disabled", the brush will trace the cursor fine, but this defeats the purpose of using a tablet pen for pressure sensitivity, tilt, et al.

Also relevant but not essential: - I have tried changing the PPI and it had no effect. - Restarting/reinstalling GIMP and my Wacom driver has not worked. - The cursor follows the pen, but the brush does not. - Brushes will follow the pen perfectly fine in other programs such as Adobe Ps.
- GIMP seems to store separate tool options (brush settings) for when I am using a pen and using a mouse and takes a fair amount of time switching between them.

Thanks for your time.