Get a new burner.
Obviously there's some kind of weird data on SD2 discs that 99% of all burners cannot write correctly.
The fact that readable data is turned into junk by the burner, makes it extremely likely that this is a hardware problem. I doubt adding the correct switch / command to CloneCD (or any other CD-R software) will ever solve this problem.
Fortunately there are a few burners that *can* write this data correctly, and thus make 100% working copies that work in *all* CD-Rom players, not just the burner itself:
Plextor 8/20.
Iomega Zip 32 (i think that's the name, it's based on Phillips hardware so there should be a compatible Phillips model as well).
Phillips 4/4/24. This model has been available under a lot of different names. AFAIK this is the only 4/4/24 burner made by any company, so if you can find a burner with these specs it should work no matter what brand it is.
I suggest you get one of these while you can.
I have the Phillips 4/4/24 model myself, and I have no problem backing up Red Alert 2 100% (Yes the copy works in *all* CD-Rom drives, not just the burner).
A lot of people don't believe this to be true but it is.
Reminds me of way back when the very first SafeDisc protected CD's appeared. I could copy them 100% right away without any problems using CDRWin and the Teac 50S in combination with a Pioneer 32X reader. For months people on various messageboards refused to believe me, and called me a liar.
Oh well, it was their loss