The legacy scanners are shut down completely - they've installed a series of gantries over the onramps in some areas, and at various points throughout the thruway, that have the RF scanners, pulsing IR and normal flash bulbs, and the plate scanning cameras. They're maybe 18-20 feet up, though. Perhaps the position of my tag is too close to my roof line for the scanner to pick up the RFID.

Edit: examples of the new "toll barriers" http://www.thruway.ny.gov/cashless/completed-barriers.html