I've been hearing this with my new CS strat. It sounds rich and clear acoustically (ash/maple wood), but too smooth when I plug in. I can't make the bridge single coil too bright if I tried. And that's odd.
I just read another post where a guy tried a new strat with Fat 50's and he described it as "muffled". Reminded me of mine.
The other thing I noticed on my guitar is when I use the tone controls, all the range is at the top and the sound turns so muddy and blanketed if all the way down. I've owned many strats and never heard anything so dark before. In comparison, my other CS strat gets nowhere near as dark/muddy with the tone all the way down.
I was going to change pickups and try 69's, but do you guys think it could be the tone caps? Where should I start?