Steve Gibson, the Middlesbrough chairman, has accepted the penalty, which also included a pounds 50,000 fine and ultimately led to relegation, imposed by the Premier League, but has been left with "a grave sense of injustice" and a projected revenue loss of pounds 7.5m.
Gibson, defiant to the end, continued the war of words by accusing the League of being "incompetent and negligent" and has called again for an independent inquiry into actions of Premiership officials.
In a 10-page letter sent to Peter Leaver, the Premiership chief executive , Gibson wrote: "Given the legal strength of your case I have no alternative other than to accept the penalties imposed on my club. This resulted in the club being artificially placed in 19th position against the true merit position of 14th in the Premier League. The consequences have been a loss in the ladder system payment of pounds 528,575 and relegation to the First Division with a forecast revenue loss of pounds 7,500,000.
"I am still left with a grave sense of injustice as I am unable to reach any other conclusion than that this incident was most certainly avoidable and that it was not avoided is due largely to the action of the officials of the Premier League both on the day and subsequent to it."
He concluded that "the attempts of my club to be heard and to receive a balanced and fair hearing have been met with a mixture of arrogance, complacency, incompetence, negligence and self interest.
"The penalties imposed defy natural justice and my club can no longer be forgiving."
A relieved Premier League, who had feared costly legal proceedings, declared the matter closed, but were disappointed by Gibson's remarks.
"The issue has been dealt with properly and fairly and it would be damaging to the whole of football if this had ended in a court battle," Leaver said.
"It is very disappointing to read of attacks being made on the integrity of the Premier League and its officials. Such suggestions have no place in this discussion and do little to the standing of those who make them. It is time to move on."
Simon Bolton, the secretary of Middlesbrough Supporters Club, supported the club's decision not to continue the struggle. "The only reason they are not doing it is because they just don't think they are going to get the points back," he said. "Let's get on with it and get back up at the first attempt. We should shove it up them and tell them we didn't need our points back - we got up anyway."
Plymouth Argyle and Chesterfield have felt the weight of the FA's displeasure at their match in February in which five players were sent off. A brawl sparked by a foul on the Plymouth goalkeeper, Bruce Grobbelaar, led to four of the red cards. Plymouth were fined pounds 30,000, with pounds 22,500 suspended until June next year, while Chesterfield were ordered to pay pounds 20,000, with pounds 15,000 suspended.
The 28-year-old Italian international goalkeeper Luca Bucci is expected to join Rangers next week in a pounds 1.5m move from Parma.
West Bromwich Albion have completed the pounds 1.25m club-record signing of the winger Kevin Kilbane from Preston, while Manchester City have secured the Ipswich defender Tony Vaughan, whose fee will be fixed by a tribunal.
Guy Whittingham, the 32-year-old Sheffield Wednesday midfielder, has signed a new two-year contract.