Well, not to harp on you, but....
Have you considered using high end audio equipment to listen to these AIFF, Apple Lossless, and the cds directly? Meaning, I am assuming you are doing all this testing on some cheesy $45 speakers plugged into your generic computer audio card (worth about $9)...you need to give us much more detail on your computer hardware as well as software that is ripping/playing.
Please detail your audio card, how it is hooked up to your speakers, and what brand/model speakers you have. It does not sound like you are pushing the music through a home stereo system.
Moreover, try this: rip your cd to AIFF or WAV...immediately burn the files to another CDR...go to a quality home stereo system and play the original cd...then play the CDR...do you notice a difference? If not, then it is something in your computer hardware setup that is altering the sound of your AIFF files in real-time. If you *do* notice a difference, then I would state that yes, something is wrong with your computer settings from the moment the music is ripped...such as equalization being permanently etched into the files...because if your CDR sounds "tinny" on your home stereo, something happened during the ripping of the original cd to make it tinny.
I have been ripping cds to WAV (I'm on a pc) since 1994...I've never had any problems.
One of the problems is that if you want great sound coming from your computer you need: 1)great sound input (cd itself, lossless file format) 2)a great soundcard (like spending $100 or more) 3)pushing the signal out of the audio card and into a home stereo receiver with great stereo speakers. I'm sure people will scream and yell that their $250 "computer speakers" are great and/or match a home stereo "system" but that's just false. My computer system has been set up with my 3-step rule above for over 15 years...it rocks. The receiver is about $400 and the speakers about $700. Audio card is about $100. But that's me...someone who LOVES music and loves a great sounding piece of music.
-Eric