Yep.

Other than that, your question requires an equally long answer, and that is that it really depends on the circuitry within the transponder but if it's designed to work at around the 4.8-6v mark, 9v is between 50 and almost 100% overvolt which could damage something. I'm not sure of the exact design or particulars of a transponder circuit but in function it is a very basic, short range transmitter.

Most IC's (microchips) are designed to work on either 3.3 or 5v (3.3 is much more common but there are chips that work on less - hence 1xAAA mp3 players and the like). Therefore, when supply voltage exceeds this, there is a regulator to keep the input voltage at the correct voltage.. 2.4ghz TX's work this way as their transmission parts also run on 3.3v. The regulator shunts off the excess voltage as heat, and has a very definite amount of power(heat) it can shunt before it goes into the state known in the trade as thermal runaway or in laymans terms "burns out"

When people leave 2.4ghz TX's (particularly those modified with 3s lipo) on for some time, such as forgetting and leaving them on overnight, sometimes the regulator which delivers the 3.3v to the transmission parts of the circuitry can partially burn out, which results in them not being able to supply the current the circuits need, which leaves the TX seemingly still working, but having almost no range.. as little as inches..

It is possible that your 9v running has done this to the regulator on your transponder. When you moved the car past the counter just you and the guy at the track, was the car closer to the counter's pickup than it had been whilst you were lapping? Try moving it past the counter at different distances and speeds.

I think "you had a couple of doubles" was just an excuse to fob you off. If the above test yields no data, try the transponder at another track.