To anyone still having this issue, I found a way to fix it; If you have opened a message elsewhere on a different platform (phone, app, etc), sometimes although the message changes to 'read' on all platforms, the desktop version still thinks you have a message. If you reopen that message on the platform that you didn't use previously (in my case, I originally opened a message on my phone, it is now showing as 'read' on all platforms, so I now open the message again on desktop), it should clear inbox (1) notification! I hope that makes sense!