Why did Skyler mess up her desk at Beneke's in season 2?
One evening in Breaking Bad season 2, as Ted is about to leave from work, he stops by in front of Skyler's office to say goodbye. Ted appears to be attracted to her, just as one might say he did when he hired Skyler back in the first place, showing no intention of thinking about it twice. Marie reinforces this idea by referring to him as "grabby hands" in front of Skyler. But it seems widely accepted over the web that Skyler is not attracted to Ted.
But in this scene, Skyler appears to deliberately knock some stuff off from her desk and her expression of frustration seems totally fake. Ted of course immediately kneels down and picks it all up. That seems like affair-kindling to me.
Although we know that Skyler later on slept with Ted to get Walt to agree to the divorce, back then, Skyler was showing no sign of intention to divorce Walt, as is suggested by their discussion and peck on the lips just as she gets on her way to pick up Ted's birthday cake.
Their tone was pretty affectionate, and this was after the scene in the office.
So what else could explain her behaviour if she's not attracted to Ted?
I don't agree with the assumption that she was not attracted to Ted. She may have left the company before due to his advances towards her but that is more likely due to the fact that she was married.
But even if she wasn't initially attracted to him, at this point in the show Walt has shut her out of his life and has been lying to her pretty heavily. Remember also that in a previous scene she and Ted shared an intimate moment where she broke down crying and they held hands.
She is reaching out and trying to get attention from the person whom she already knows is likely to give it to her. So she knocks the pens off her desk because she wants attention and companionship.