It was a running gag between the Puerto Rican born Chairman of the committee and the Supreme Court Justices testifying before him. It had been going on for more than ten years. Congressman Jose Serrano was chair of the committee responsible for Supreme Court funding and would tease the justices about his presidential eligibility...because he was born in Puerto Rico. Thomas was jokingly evading the question of Serrano's eligibility to be president. Obama never came up. The same thing happened before Obama was even a candidate.
This is but one example of the many birther myths that still persist.