That has happened to me on numerous occassions. The card reader is very sensitive (much more so than the subway card readers). Generally, I don't put more than $5 on my card and if the machine deducts the money without letting me through, I go to the attendants that will check my card, see that the fare has been deducted, and let me pass. Unfortunately, it is a real pain in the a.s adding only $5 at a time, particularly if you have multilpe trips coming up.

Also, I agree that taking down the intra terminal line during the day is also a pain. Particularly for me because I can get off at Term 1 and transfer across to the intra terminal train, stopping next at Term 8, AA's terminal.

But the JFK Airtran beats the EWR Airtran anyday even with those quirks and hey its the Port Authority running the show.