The Progenitor was programmed to recognise only genetically pure Daleks. The "Ironside" Daleks of "Victory of the Daleks" were not genetically pure Daleks, as the Doctor said & as they tacitly admitted.
The original Daleks -- the Daleks' standard of genetic purity -- had been genetically engineered by Davros from Kaleds who had already been mutated by exposure to the weapons used in the Kaled-Thal War on Skaro ("Genesis of the Daleks"). The Daleks were descended from Kaleds but they were a new & quite different species. To the Daleks, all non-Dalek DNA -- including Davros' own Kaled DNA -- is "inferior" to Dalek DNA. Davros built that outlook into them when he created them & the Daleks, in turn, programmed it into the Progenitor.