I've been fighting this issue for months. The issue transitioned from Lenovo X230 to Surface Pro 3. From Office 2010 to Office 2013. The only thing that seems to fix it temporarily is repairing the office installation.
1. Presentation file open
2. Slideshow started
3. Highlighter pen enabled with CTRL+I
4. Draw test with highlighter done
5. Screen cleared with E
6. Computer idle for about 5-10 minutes
7. Go to draw with highlighter, it seems like now the PEN mode is enabled, drawing on the screen doesn’t work. The pen pointer on the screen follows the physical pen pointer. Touching the screen, advances slides instead of drawing.
8. Enabled highlighter via CTRL+I, highlighter icon shows, follows physical pen , does not draw.
9. Press CTRL+I again to enable highlighter pen, PowerPoint bring up an error message. “We’re sorry, something went wrong that might make PowerPoint unstable. Please save your presentations and restart PowerPoint”