For the simple explanation; The on-board chip and pin machines go by the information contained within the chip. If the bank have set the information in the chip that they want a "telephone" authorisation of your card at every (or the next) use, then, as the on-board chip and pin machines can't do this, it will come up as declined as there is no telephone authorisation. You may have several million in your bank account, but the card has no way of telling this.
To prevent it happening again, you need a card that is authorised for "off-line" transactions.
If you had paid at the booking office, then it would have been accepted. Unfortunately, although there are several excuses that can be accepted for being on-board a train without a ticket, walking past an open booking office because you were late is not one of them. You had committed a bylaw offence by doing that. Being unable to pay (for whatever reason) has now compounded that mistake, as it sounds like the guard was prepared to overlook the initial offence, but you placed them in the position that they had to report it further.
Wait for correspondence from the TOC, but you may be looking at a large financial penalty to either keep it out of court, or pay a court fine. I'm presuming he took your name and address?