Not applicable to the S, but in the new MX owner's manual (not sure if it was in the old one) it instructs you to put the transponder on the panoramic windshield above your head. Has this worked for anyone?
I put my EZPass all the way at the back of the windshield in the center next to the channel on my X, and it seems to work reliably there. I'm not sure if newer S windshields use the same coatings as the X or the older metallic coatings, though.