This is because various CDs in your collection are mastered at different levels. Normally Sound Check would be able to address that, but during the past ten years or so, artists have begun to master CDs so they sound "loud" all the way through (e.g., even during the quiet parts), at the expense of dynamics.
This video explains what I'm talking about better than I can:
www.youtube.com/watch?v=3Gmex_4hreQ
If this is indeed the cause of your problem, sound check isn't making a difference because it's only measuring the peak level of every track. Tracks that have been mastered properly (so the quiet parts of the song actually play back at a lower volume than the loud parts) are going to sound quieter than tracks that have been mastered to sound loud all the way through.
I’m sorry that I don’t have a solution; other than some two-bit advice: newly remastered CDs don’t always sound better than their 80s counterparts. They’re just louder, and for those of us with the ability to adjust the volume knob ourselves, loudness has nothing to do with sound quality.
en.wikipedia.org/wiki/loudness_war
Also, it certainly wouldn't hurt to write to the artists who put out the CDs in question (and their labels) and tell them that you object to the way their CDs are mastered. If enough people complain, they might begin mastering their CDs to a better standard.