In my first playthrough, Gene showed up early on, and I failed the Charisma check to buy a dog.
Later on, around level 90-something, I really wanted some dogs for the settlements. But Gene was nowhere to be found. I wasn't finding him in any random locations others had posted. He wasn't visiting Sanctuary, or Abernathy Farm (which seemed to be his most common spawn point). Even console commands were not bringing up the "right" Gene - just a non-communicative clone. All the cheating I could do wasn't working.
So I just started dropping dogs into my Sanctuary using console commands. That worked. Lots of dogs running around Sanctuary. Fun times.
Then, at level 100, I just randomly stroll back into Salem
Spoiler
Gene.
Somehow the turrets were targeting him and his current dog. So I shot them all down
Spoiler
I'm wondering if he was just kinda logic-trapped in Salem this whole time?