I dunno. I think it was because Mulder did seem to gravitate towards the fowl one as someone who would share his viewpoint, even though it may not have been the best idea. Plus, it was like she swooped down and went after him full throttle sometimes. Also, I think that Scully seems to have an inherent jealous streak... see Bambi and the cop from Syzygy.

And yeah, that Touchstone moment was pure gold. :)