As I said, rip the track to Apple lossless (or WAV or AIFF) using iTunes. If the problem still persists then it can mean the later two things I listed. You can completely eliminate iTunes if you use EAC or dBpowerAMP to rip the CD to a lossless format. Compare that lossless rip (both can rip to Apple lossless, dBpowerAMP more easily) with the rip that iTunes completed. There are many utilities out there that can examine both files and determine if they are identical. If both files are bit-for-bit identical, then it means that iTunes is not the culprit.
On a side note, you should download foobar2000 and conduct a blind ABX test between an iTunes ripped lossy file and a lossless file ripped with another program. Failing the ABX test would mean that the sound difference you are hearing is in your head or iTunes is not properly decoding the tracks.
First and foremost though, you should rip to WAV with iTunes and then download dBpowerAMP (you can download a free 14 day trial) to rip to the WAV format. Compare the two files (foobar2000 can do this). Listen to both files in iTunes and outside of iTunes as well. If the files are identical and play fine both in and outside of iTunes, it means that your track/s are actually suffering from lossy audio encoding or you are hearing things (the later is known as the placebo affect and is very common, it is not an insult).
64GB iPhone 5 | 64GB iPad mini | AppleTV 2 (2012) | AppleTV 2 (2010) | 2012 15" MacBook Pro, 1TB SSHD, 16GB DDR3 1600 MHz, OS X 10.8.3 Mountain Lion | Apple Lossless | iTunes AAC 192kbps VBR | iTunes 11.0.2| Library size = 1.04TB | Legacy iPods: 3G 40GB, 4G 40GB, 5G 60GB, 160GB iPod classic (2009)