It could also just be a transponder that is going bad. I had the same thing happen to me once. I pulled my hair out trying to figure out why it dropped a lap once in a while, then on day it started dropping almost all of the laps. It still registered sometimes but not most of the time. I sent it in to AMB and they replaced it with a new one for half price. Mine was like 4 years old so no warranty any more. Mine was mounted flat to the chassis too when it went bad on me. Being mounted flat to the chassis is very hard on the little transponder and it takes quite a hard beating that way IMO. I know there are transponder testers that you can set the transponder directly on and it tells you how strong the signal is. If you can find one of those it could tell you if the transponder is bad, or just something in the wiring /positioning that is causing a weak signal.
Good luck with getting to the bottom of this, its a frustrating thing to diagnose.