From the OP's story he failed to present himself at the gate in a timely manner. The airline is not responsible for paying compensation in these circumstances.
The regulation (as amended by ECJ judgements) applies when a flight is cancelled, or delayed more than three hours. Neither of these appear to the case here. It also applies to 'denied boarding' which doesn't appear to be the case either, as the passenger never arrived at the gate.
The fact he was prevented from doing so by a third party is irrelevant to the airline. Any claims for damages should be presented to the airport/security company. (A little clarity on where this happened would also have been helpful)
The 'differences' in the documents are likely as the airline quoted the Regulation as adopted by the Parliament and the Council, while the EC site (got a link?) probably embellishes that with their interpretation of how ECJ rulings may affect the Regulation (something the ECJ has not done.)
In any case this was not an delay of more than three hours caused by the airline. R261 does not apply.