Murphy spent nearly two years in jail.
In 1968 he was the driver and lookout man in a scheme to rob Olive Wofford, a Miami Beach socialite. He was also charged with first-degree murder in the "Whiskey Creek murders," the 1967 case of two California secretaries who were found shot, bludgeoned and dumped in a creek north of Miami, concrete weights lashed to their necks.
Murphy denied the murder. But in 1969, he was convicted of killing Terry Rae Frank, 24, and sentenced to life in prison. In 1970, he received a second life sentence, plus 20 years, for conspiracy and assault to commit robbery against Wofford.
On Thursday, Murphy again asserted that he did not kill anyone, saying instead that he was driving a boat when an argument broke out and the women were shot after they threatened to go to the FBI.
"I hear bang-bang," Murphy said. "It was an absolute train wreck, a nightmare."
Scott said after the meeting that he did not know about Murphy until the clemency case came up. But he said he "felt positive" about granting Murphy's restoration of rights, which would have allowed him to vote and serve on a jury.
Murphy's bid to win his rights was backed by former Florida Department of Corrections Secretary Louie Wainwright and others who spoke about his years of prison ministry work since he was released from jail in 1986.
Murphy has gone to prisons across the country and abroad while working for Champions for Life, a prison ministry founded 35 years ago by the former Cleveland Browns football star, Bill Glass.
After the vote, Murphy said he had hoped to get his clemency request granted but he had expected the outcome.
"It's the nature of the times," he said, adding that he was surprised that Scott sided with him. "It is what it is."
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