FWIW I was there as well. Pitting with/next to Dan and Mike. My transponder did the same thing as did another guy in the same heat whose didn't count at all. After a little asking around it became apparent that this has been an issue before at this facility. Not sure what the reason is but I don't think it is your transponder Dan.
From what I gathered Dan didn't change anything all weekend. His car went from counting perfectly to only counting sometimes, same as mine and everybody elses that had a problem. I do know that the director rebooted the computer several times during the day. Not sure if this had anything to do with the apparent issue or not. He did tell me via "the red phone" that this happens alot with the E-Buggies.
I think you should try to race at Indy Tuesday night and see what happens. My money says that it works just as good as it did before you left based on the other issues that happened over the weekend.