When you get a chance, take it apart again, and look at the piece of the shifter that contacts the grooves, in the pics you have shown here. As it is working now, I wouldn't worry too much, but there has to be some wear in something, to pop a rail forward, and not be able to get it back, with the shifter...
After looking at the very first picture, of the 2 shifter sticks, I think you may have an alignment problem, not sure... Can you rotate that left hand shifter through a wide arc? In the pic, it looks like it skews way to the left. All my kubotas have a rigid stick, with no arc type movement. Could have a pin missing or broke off, never have taken one apart , so I'm not too sure...