O.k. let me see if I can esplain this, I have a Eclipse tank bag, it's huge, on top is a compartment with one zipper on each side. One can store things that are flat like, the rain cover for the bag, tire plug set, phone, map etc, on that flap is a nylon mesh pocket when the flap is closed the mesh is on the top of the closed pocket not exposed. I store the ez pass transponder facing the opposite direction that it would be facing if installed on a windshield because, the Velcro strips grab the nylon mesh and holds it in place so, your theory that it has to face a certain way does not hold up under the above conditions, sorry !
There has to be another reason why it's not working.