Also reproducible in 3.14. I'm about to get the latest version (3.14.2 at this time) and try again.
Update: ...Not fixed in 3.14.2. Arranged my docked dialogs as I want them and closed 3.14. Updated program (running standalone JAR on Windows) and reopened, dialogs are all dumped into a tabbed panel on the left side instead of how I left them. (Not 'Structure View' though...). Re-arranged and closed and re-opened again, and everything is once again piled up over on the left.
Now trying the 'delete user prefs' suggestion from the 05/27 comment.
Update update: Well there's no option in the UI called 'Delete Preferences' or any variation thereupon, but I tried 'Reset Layout' from the Windows menu, then recreated my desired layout, then restarted. It was discarded again. Also tried deleting "yed-3_5.layout" from my %AppData%\Roaming\yWorks\yEd, and even deleting everything from ...\yEd\, both to no avail.