New Neck... New tone?

A couple of months ago I put together a parts telecaster. All Parts Alder Body, Lollar Pickups, Joe Barden Bridge. Pretty quality stuff. For the neck, I used an old replacement Tele neck I had sitting around. I bought about 15 years ago, so I can't remember the brand. It was a maple with Rosewood board. I never really liked the neck the neck that much, but I put it on just to get the guitar going until I found neck that I liked. Last week I won an American Standard Tele neck on ebay... again rosewood on Maple. I put it on the other day. Last night I tried it with my amp for the first time.
I don't know if I am just imagining it, but it seems like the whole frequency response of the guitar changed compared to what it was with the old neck. I feel like there are much more low mids, maybe even as much of a 2-3db increase around 200-300 hz range. The guitar sounds fuller bodied, but now it seems muddier on the neck pickup. I had re-adjust my tone controls on my amp. Is it possible that a new neck could affect the tone of an instrument that much? The american standard neck is a little meatier, so it probably has a little more mass. However its the same types of woods... However obviously not from the same trees.

Any other experiences with this? Would a different neck really change the tone that much or am I imagining it?

 

Well this sucks, because now instead of solving my problem with a new neck that I like playing, I now have a new neck that I don't like the way it sounds as much. The old neck was much snappier, crisper, but was not that fun to play.
I guess it makes more sense that the neck would have a bigger affect on the tone then the body, as majority of the string vibration is being transfered through the neck before hitting the body.
Also, The butt of the neck didn't sit perfectly flush against the body. Its the small area perpendicular to the fretboard, facing the pickups, would that have much affect on the tone as well? Less surface area for string vibration transfer?