if you have no luck go to the ryanair cutomer services desk or see swissport in STN. The boarding pass should be denied by the gate staff if they are on the ball and doing their job properly. You can only travel web check and go by providing your passport no, even on domestic flights.
Usually the staff will charge you the £3 fee, and you'll have to take it up with Ryanair in writing. This is usually the case. I know its a system error but the staff at the airport can't just take your word for it, so they may hav to follow the rules and charge - thats normal ryanair (handling agent) practice.
Hope it all gets resolved - the new skies system is just a joke!!