Hi Mike,
we haven't heard of such a problem before. Since it works fine in the same session but the settings are gone after logging out, this might be a problem with the system folder protection in Windows 7. As far as I know, this feature silently redirects access to certain protected directories to a temporary location which is cleared on log-out. However, recent versions of yEd store its preferences in the designated location for application settings, in the folder %APPDATA%, which shouldn't be affected by this. Are you using the latest version of yEd (3.8)?