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Looks like you've already tried the obvious things that generally help sort these types of problems:
- reset InDesign preferences
- ensure you have latest driver for tablet installed.
- another thing to try is disable other third party plug-ins for InDesign that might be installed (but I doubt that'll fix the issue you are seeing to be honest)
I'm not sure if this will help, but apparently Windows 10 'Anniversary Update' has added new pen controls to the system. If you happen to have installed that update, maybe the answer is to be found in the configuration of these (Devices > Pen & Windows Ink, deselect the Use Windows Ink option if it is selected).
Well friends and neighbors, the issue is solved.
I noticed that I was having some weird pen issues with Word and Excel too. So that made me think that something is out of whack in the operating system - since the drivers were up-to-date. Turns out my machine had not been receptive to Windows 10 updates. I ran the Windows Update Troubleshooter: https://support.microsoft.com/en-us/instantanswers/512a5183-ffab-40c5-8a68-021e32467565/wi ndows-update-troubleshooter and was subsequently able to run the Windows updates to get me up to the latest version and ... Viola! All is back to normal.
I'm having the exact same issue, but the suggested solution doesn't work for me. (I have most up to date Intuos and InDesign drivers/software. Windows 10 says it's up to date too.) The Windows Update Troubleshooter isn't solving any problems. (Photoshop works fine, I should add.) It seems this happened with the most recent InDesign update (?). Anyone else seeing this issue? To repeat the problem, the mouse works fine. The touchpad on the Intuos works fine. But when the pen "clicks" on anything in the page, be it an image, text box, etc., the software freezes--the cursor still moves when you move the pen, but the screen is otherwise frozen. As soon as you grab the mouse, it returns to working fine.
If no suggestions, I'll revert to the previous version of InDesign and see if that works.