OK, I agree there seems to be something wrong with your second file. HOWEVER, I don't believe the audible difference has to do with anything that happens between 10-16KHz.
Technically speaking, Mutant nailed it. What you're seeing on the picture is the combined noisefloor of your DA-AD conversion (DA in the cd, AD in the soundcard), and your cd player's low pass filter at 16KHz. Have you tried the same thing with another cd player?
Then I am really freaking stumped because that's all I can think of it being. As I said I did add a hi-shelf at around 6khz and dropped it a ton (almost -12 db) and it did have some effect on the, at least, percieved disruption in the guitars.
I have tried two other CD players. One did it just about as much and the other didn't do it until the volume was at or near peak volume.
BTW I really appreciate everybody's input and help thusfar! It's really appreciated