Later when they did find small differences they think those differences could be from "jitter" differences from different production runs, but store CDs may just as likely be the worse ones.
Also when I got married, my wife and I had some duplicates (mine clubs, hers from the store), so I did my own test. I used a changer as a transport for the DAC and had her put the CDs in, so I would not know which was which. I could not tell either for the few I tried.
And finally, some CDs are just defective from production, even though the record companies claim it can't happen. I have returned CDs before because of defects (store and clubs both).
A copy of the Stereophile article is at:
http://www.stereophile.com/showarchives.cgi?55