Tough question. I started watching the show during the sixth season (my first episode was How the Ghosts Stole Christmas) so I was kind of watching the series forward from there and catching up retroactively at the same time. So, it's possible some of what I saw in the sixth season leaked into the way I saw earlier episodes.

Though I was only 12 when I started watching and even though I was reading all the lusty fanfiction, I don't know how much I thought about any of this at the time.

But definitely now, when I take in the show as a whole, I can't imagine Mulder and Scully not sleeping together after the third season. It totally makes sense in my head, I swear!