I have to agree with Maggie Helwig here. I fail to see how Karen Berquist represents any kind of barrier at all to Scully. In fact, it is disappointing that we don't get to glimpse Scully's compassion here, as she frequently develops a bond with the various sufferers of the world. That Karen addresses Mulder as Fox is not surprising to me. He isn't invested, so it's perfectly safe for Karen to call him Fox.
Alpha makes an interesting comment on gender.
Mulder only feels misled by Karen when he realizes she has lied about the case. In fact, there is a tie-in between the killer dog and the relationship trickery. Only men are tricked by the dog in the episode. Well, the truth is I enjoyed watching it, bad dog jokes and all.