I didn't have the minimize_to_tray option set in the past, but now we have tabs I've decided it would be useful.
With minimize_to_tray on, if you have two windows open and you minimise one then it disappears, never to be recovered again! "Show window" from the tray icon just shows/focusses the remaining window and if you minimise that too then that that's the only one pulled up.
Assuming the 1st minimised window still exists, I think the easiest solution is that "Show Window" on the task bar icon menu or clicking the icon should reshow all windows, perhaps it can be named appropriately, however in doing so I think the shortcut intended to show window should still just pull up the last used one.
David