If you don't mind describing your card - I have had similar problems and I am trying to get a sense of how common it is.

I have a Bank of America Visa check card (not a "real" credit card) and the one time I tried to use it, at Harvard, it wouldn't run in any of the (working) machines either as a debit or credit card. There was an MBTA employee right there to help people with the machines, as they were newish at that point, and her attitude was that it was my problem and not theirs.