My problem with the line from the pilot is that it does't sound better in the head than it does out loud. It sounds very much like a man writing a female character - and getting it not quite right. For me, this creates a canonical problem because I just can't imagine Sam actually saying this, even though she did.
I think it gels fine with Sam's character in Season 1, which gradually becomes less intense and fits in more once she realizes no one cares what gender anyone else is. And I guess I'm in the minority, but I love that line. I fell in love with her in that scene, so... *shrug* It made sense to me that a female in the military would feel a male officer was looking down on her because she's a woman.

And I still don't know how to explain the Mulder line except that he meant he wasn't a practicing psychologist, but then it still totally contradicts his whole profiling history anyway, so it was just randomly wrong.