While George Bush was delivering his keynote speech, demonstrators trickled out, complaining of being held in a bus cleaning station beside the Hudson river without access to lawyers.
Many of those held in what protesters have branded "Guantánamo by the Hudson", said they were not involved in anti-Bush demonstrations but had been swept up by overzealous police.
They included the manager of a theatre who was coming out of a subway station with a friend on their way to celebrate his birthday, and two women who had been shopping.
Tobi Starin, a teacher in Rockville, heard from a friend that her daughter, Liz, had been arrested while coming home from work. "I kept thinking, 'She'll get out any hour now,'" Ms Starin told the Washington Post. "But it's 44 hours, and she's still in there."
Police arrested 1,700 people during the week that was full of protests but devoid of the violence that many had predicted.
Late on Wednesday night, Judge John Cataldo said the detentions violated state law. Early on Thursday afternoon he threatened to impose a fine on the city of $1,000 a day for each person kept in custody longer than 24 hours without being arraigned. By late on Thursday he was still not happy with progress.
"We're coming back again until this is settled," he told city officials. "Once again, the order is, release these people."
City officials say the sheer number of arrests caused a delay in processing.
The deputy police commissioner, Paul Browne, blamed the demonstrators for overwhelming the police. "It's a new, entitled, pampered class of demonstrators, who want to engage in civil disobedience but don't want to be inconvenienced by arrest processing," he said. "There's a lot of reasons for a hold up. If you were in a group this morning, you are going to go through the process very quickly; if you were arrested with 200 people, it's going to take longer."
Some protesters emerged from the facility holding their fists aloft and claiming victory. Others, who said they had been denied medicine for asthma and epilepsy, sat on blankets in a park across the street and sought attention from doctors who had been organised by activist groups.
The doctors said they found several cases of rashes and skin infections, apparently as a result of cuts from overly tight handcuffs that were exposed to chemicals.
They were asked to collect samples of clothing to test for exposure to toxic chemicals.