I don't think she thought it was Patrick necessarily, just that it was possibly her husband was cheating with a man.

Valeria believed it to be Patrick becuase she saw herself in his decriptions of his partners wife aswell as already being insecure becuase John had done it before, and because he'd been spending more and more time 'at the office' and wanting to drive alone, because he was in fact going to the ally waay where Elenor died

It was never said for sure why Valerie thought John was the guy Patrick was talking about.
However, I believe she felt that way because she was already insecure. As a couple, they had clearly fell away from eachother after their daughter died, and he clearly didn't want to be around her. She felt insecure and began to suspect there might be another woman, and if you remember at the end John admits to Leon that there was another woman years ago and Valerie had never regained her complete trust of him.
Then this Patrick comes in her office acting all creepy and she began to suspect it just because she was already looking for there to be an affiar
However, this is just my opinion, so don't take my word for it!