Reproducible in Chrome and Firefox. Not reproducible in IE11.
Dojo example.
There are two Menus. In the first one navigation is triggered from the function passed to the "Sub Item 2" item's url option. In the second Menu navigation is triggered in the Menu's select event handler.
Doing this in the first Menu, results in the submenu remaining open.
The submenu should close in both scenarios, since closeOnClick is enabled by default and the select event fires before triggering the navigation.