> So long as your CD doesn't include any square waves, you're golden.

Could you explain what you mean by this? Are you referring to certain patterns that fall within standard Redbook audio parameters that FLAC then fails to encode properly? Or perhaps to characteristics of CDs or CD playback equipment that are difficult to duplicate on modern-day computers? I can imagine something like preëmphasis being problematic sometimes, but that seems to have little to do with square waves.