Hi WH,
I had a similar problem a while back. Only thing I could track it down to was the combination of the laser power in my in-car CD player and the lower reflectivity of CD-Rs. I.e. my car CD-player's laser was not as powerful as my home & PC players and the blue tint of CD-Rs can make them more difficult to read. Usually only a problem for older players, maybe worth trying one of those specialist lens cleaning CDs - I know some folks do not recommend them but I have found them to help.
Good Luck