If you recall, Stan was suspicious as hell in Season 1 Episode 1. But then he was scolded by his wife and was eventually seduced by the Jennings' charms. Phillip is his best friend now, goddammit. Do you question your best friend's ever move and intention? If so, I think your "friend" should find someone new to hang out with. Bastard.

Yeah Stan was poking around their garage and car in season 1. He had spent three years as an undercover working against the KKK and thought it was really just PTSD after his first wife divorced him and told him he took the loyalty thing too far when refusing to discuss what he did at work. I think the girlfriend is KGB too. Maybe she was put their to protect the Jennings. But if that's true, wouldn't she have known that he was sniffing around their circuit box and trying to take a look at the basement? There's only three more episodes and we haven't seen anything from the girlfriend!

In all fairness, the groundwork was laid for this final realization in season six. As others mentioned, he was suspicious in season 1. Then incidents began to pile up such as the bio-scientist essentially describing Philip and Elizabeth, hearing that they don't have any relatives, their frequent disappearing acts and very odd hours... I forget what it was that finally tipped him off but it snowballed during season six until he reached the right conclusion. If you think about it, it would have to be a helluva a leap to think your neighbors and best friends are communist spies. If anything, I think the last season (which was only 10 episodes long) was a little rushed. I think they could have spent a little more time on Stan's slow and begrudging realization.