Yeah, I noted the pickups. But still, it could be the guitar without it being the pickups. Or it could be the EQing needs fiddling with, or any number of things. Or the amp could suck. ;) But, like I said, I really think that the tone was better in the first clip. Well, at first it was, but the bridge position was pretty brittle and yuck. But I still think it sounded clearer and more open than in the second clip.
Have you played your guitar through any high-end amps? If so, which ones and how did it sound then?