John,
If I'm not mistaken the "Have Yourself a Merry..." is the LAST track on the James Taylor "October Road" CD. This is important because it indicates why you were having problems. Unlike a TT, the CD plays from the center outward, so the last track on the disc is on the outside of the disc, with the TOC closest to the disc's edge. If your CD drive or your PC isn't quite up to snuff you'll have more problems ripping the cda file at the outside of the disc, i.e. the last track on the redbook CD. You can reduce the chances of this happening by reducing the speed at which you extract audio from the CD. I find that Exact Audio Copy (EAC) often extracts audio at 8X or less from my Plextor 48X burners. Next time you're ripping a disc, watch to ensure your extraction speed doesn't exceed 24X. Also, try not to run any other software on the PC while you're extracting audio. If Windows takes an interrupt at an inappropriate moment, you'll get a digital glitch in the wav file, and it might be audible in the way you describe.
As for your copy protection theories, the James Taylor "October Road" redbook CD is not copy protected. Most "real time" CD recorders (as in stand-alone audio recorders like the Philips or my Marantz CDR-630) will probably ignore any copy protection on the disc because it has to play the disc back in real time. Thus the digital stream from the CD can be copied in real time onto recordable media. Where problems are going to occur is in the kind of copy protection that writes a "digital watermark" on each track, which is supposed to be degraded when copied, leading to audible artifacts when the copy is played. Earlier copy protection schemes worked by putting invalid data in the CD's table of contents (TOC) at the outside edge of the disc, which would cause a computer-based software package to crash or indicate the disc is unreadable when attempting to rip the CD. That's why the copy protection could be defeated by drawing a thin black line on the outer edge of the disc, obscuring the TOC and the erroneous data deliberately placed there.
As convenient as CD copying is on my computer, I'm going to hang onto my Marantz CDR-630 so i will always have the option of burning discs in real-time from the digital output of my CDP, just in case I want tracks from a copy-protected disc i might buy.
