CDs are expected to be flawed, regardless of scratches. Part of the reading process is in correcting those errors. It's possible that the two drives correct the errors in different ways.

Data CD filesystems also expect there to be errors, and are encoded with a real error correction algorithm (IIRC, it's actually two or three passes of Reed-Solomon) so that you can get the exact data back off of it. Audio CD data has no such facility and expects the CD player to fill in the blanks based on no additional information -- just extrapolation from surrounding data, I guess.