I have this exact problem. I just ripped several CDs to flac using Express Rip CD Ripper Software Plus (licensed version) and every track is oversaturated and distorted to such an extent as to make it inaudible. The CD plays fine in a computer and on a CD player. Also, at least one of the CDs is older, manufactured before ripping was prevalent, so I am skeptical that copy-protection is to blame. The CD copy protection schemes I am aware of altered the table-of-contents information and affected a CD-ROM drives' ability to read the disc at all and could not carry the Compact Disc logo.
To answer Chris75's question, I used both maximum compression (4) and "Balanced" (2), the default. Sample rate of 44100 Hz, 16-bit resolution (standard CD).
Please advise.