There are a lot of "one of those things" with JMRI on a RPi with VNC. A favorite of mine is the JMRI windows which open at the top left of the VNC screen and hide the window title bar so that it is impossible to move the window. My workaround is to place the RPi menu bar at the bottom of the screen so that I can maximize the window from the menu bar. That restores the title bar and I can un-maximize the window and move it. The other favorite is that I have noticed that the Window menu in all the JMRI windows does not bring windows which are hidden behind other windows to the foreground.
--
-Ralph