Sry i carn’t reproduce that same problem on my Mini Mac (M1) and B/T Logitech Mac keyboard with Sonoma 14.3.1.
Could be something going on with your Mac book keyboard or something differant in the OS. Dunno. Unfortunately I don’t have a Macbook to test. Other users though on this forum can give feedback on that if they have that same issue.
The only thing i can suggest is eg: Try uninstalling eM Client via “first closing eM Client” and then dragging the eM Client icon from “Applications to the bin”, and then reinstall V9.2.2230 via the release history page. Removing eM Client from the Applications folder doesn’t delete the database, it just removes the actual program part of eM Client.
Or try the updated new V10 Beta which i have also been using which also works fine for me with the Command w key. Also has alot more features and user requested options added as well. If you do update to try V10 Beta, make a manual backup of V9.2.x first via “File / Backup”.