Let me just say, your post helped me, because I realized that I was not going crazy. But, I was able to find the manual on this frigerator, which was key. There was one phrase in the manual that gave me help - "when the glass shelf is pushed to the rear, it will align the rear latches.
Manual from whirlpool website:
http://shared.whirlpoolcorp.com/assets/pdfs/literature/MSB2154ARA.pdf
So, the rear latches must be installed in such a way that the sliding glass shelf not only touches them, but pushes them into the correct position.
This fact helped me to try different positions, each time testing to see if the glass shelf would do anything. Finally, I realized that there is a triangular shaped part of the rear latch. The hypotenuse of the triangle is what comes into contact with the little nub on the underside of the glass shelf. The nub on the glass shelf pushes the rear latch along the hypotenuse of the right triangle, and into the correct position.
Here is a picture of it installed in my frigerator,which I am sure will tell it better than any words: