I'm regularly experiencing a similar issue on Windows 10:
Screenshots do not make sense in this case, on the other hand, I'm happy to look into the logs (and run it in verbose logging mode) if you'd like me to.
Thank you very much for the detailed information.
Since this problem occurs only on Windows, it could be related to the Windows look and feel. Would you mind testing if the problem does not occur if you use yEd's cross-platform look and feel? How to use the cross-platform look and feel is explained in Is it possible to switch to the cross-platform Java look-and-feel?