To Quote the Architect:

"The matrix is older than you know. I prefer counting from the emergence of one integral anomaly to the emergence of the next, in which case this is the sixth version."

"The first matrix I designed was quite naturally perfect, it was a work of art, flawless, sublime. A triumph equaled only by its monumental failure. The inevitability of its doom is as apparent to me now as a consequence of the imperfection inherent in every human being, thus I redesigned it based on your history to more accurately reflect the varying grotesqueries of your nature. However, I was again frustrated by failure. I have since come to understand that the answer eluded me because it required a lesser mind, or perhaps a mind less bound by the parameters of perfection. Thus, the answer was stumbled upon by another, an intuitive program, initially created to investigate certain aspects of the human psyche. If I am the father of the matrix, she would undoubtedly be its mother."

Possibly v1 & v2 also had Ones? The Architect speaks of the anomaly being ineradicable despite his best efforts, in which case it would be present in the eutopia and dystopia versions too. This would explain why the Architect speaks of each version being identified by its anomaly, yet also says 'The first Matrix I designed', regarding the eutopia version, i.e. v1.