Hi Huw509,
We appreciate you raising this concern here in Microsoft Community. Based on your post, we understand that you're experiencing issues with using your Surface pen during PowerPoint presentations on one of your devices. Allow us to check this further and help you sort this out.
Just to confirm, since you mentioned that it works fine on the other PowerPoint app, may we know if they have the same build and version of Office. To check, you may refer to this article.
This issue may occur due to a defective add-in installed on your app. To isolate this, let's try launching the affected PowerPoint app in safe mode. This would help us identify if an add-in or extension is causing the problem.
- Find the shortcut icon for your Office application.
- Press and hold the CTRL key and double-click the application shortcut.
- Click Yes when a window appears asking if you want to start the application in safe mode.
Also, when you mentioned that there's no Pen option in the Advanced settings in your PowerPoint, may we know if you're referring to this setting:
To notify us and have us get back to you, simply reply to this post.