The parenthetical is evaluated separately from the sentence. It would equally read this way:
He's definitely a weirdo at times but he's a good guy, (I mean that in a positive way, for instance he likes old movies and watches them constantly, but when he says a movie is good he has never been wrong)
as the way I originally wrote it:
He's definitely a weirdo at times, (I mean that in a positive way, for instance he likes old movies and watches them constantly, but when he says a movie is good he has never been wrong) but he's a good guy
The "but he's a good guy" never syntactically follows the information about the movies, it is always tied to my opinion that calling my friend a "movie fanatic" isn't a strong enough descriptor and he teeters on the verge of being weird about it.
