Oh, I think I misunderstood your question.
I am hearing the potential glitch when listening to the original cd, the ripped wav, the flac (lossless) encoding, or the ogg (lossy).
I'm using cdparanoia to rip the music, and multiple runs of cdparanoia produce identical results. So I'm confident I'm accurately getting the data off of the disc.
I guess the questions I have are:
1) is there any way to be sure something is a glitch in the actual physical cd? Without access to another copy of the same disc, I have no easy way to compare. Is there anywhere to go with, say, an md5sum of the ripped track as a wav or similar and compare with a known good value?
2) is an actual flaw in an audio disc likely? (Say, 2 of the last 10 discs I have purchased.) Such a high error rate seems odd to me, given the needs of, say, a cd-rom for perfect reproduction, but I have no idea what kind of error correction or checksumming is inherent to an audio cd.