Magistrate Phindi Norman said she was "confused and astounded" by the State's decision to refer the case back to the Director of Public Prosecutions, to decide if the prosecution of Uys is to continue.
Uys, who's referred to in the corridors of the court as "the Scarlet Pimpernel of Cyberspace", appeared in court again on charges of fraud and crimen injuria.
The charge of crimen injuria filed against Uys by Simon Grindrod of the ID relates to an internet sex blog by a male prostitute, in which prominent South African men were named.
The charge of fraud relates to a case involving R250.
Nothing linking Uys to charges
"I wondered what was going through the Public Prosecutor's mind," Norman said of the decision of a previous prosecutor to go ahead with charges against Uys, bearing in mind the content of the court affidavit.
The magistrate postponed the case for the last time and gave the State until September 21 to decide what would become of it.
Uys's attorney Reaz Khan put it to the court that he and a senior prosecutor had examined the contents of the dossier and agreed that it contained nothing that could connect Uys with the charges against him.
Khan said he had met the prosecutor on Monday morning specifically to see if there was a case against Uys. "Everything is based on the suspicions of the complainant and on media reports," Khan told the court.
He pointed out that Uys was not named anywhere in Grindrod's statement as the person who committed the offence of crimen injuria against him.
'Previous charges not true'
"In the 10 or 12 years that I've been in the public eye, there have been 15 similar cases against me. Not one of them was true," Uys said.
Some of the cases in question include possessing child pornography, and the murder of a friend in Kroonstad.
He said this was his first time in the dock.
On his being connected to the sex blog, Uys said the Gay and Lesbian Alliance (GLA), which he formerly led, did not even have a webpage.
"If I'd been such a boffin on web pages, surely that would have been different," Uys said.
And is he the real Neil Watson, who started the infamous crimexposouthafrica (Cesa) website?
"Neil Watson is in the USA. As far as I know, he's still involved with a new website," Uys replied.
Rumours had it that Watson was an alias used by Uys.