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hmm, ill have to try that when i get my gs2 back (a friend has it)...
nope codebreaker doesnt. at least 4.0 doesnt
SwapMagic's work great for PS2 Games if you've got a swap-mod chip. (DVD disc has 4.35 TOC Though, so larger games like DMC may have trouble)
As for CloneCD--it has never failed to burn my PSX or PS2 CD's (once I got the right settings). Make sure your hardware is compatible and the settings are right. Also, make sure you're not trying to break the speed barrier when you read the image or burn the copy. I never exceed 4X with mine--have even had success burning the copy on the fly up to 4X with version 126.96.36.199.
If you are burning from a downloaded file, it may be a problem with the file itself (PAL/NTSC version, Patched/unpatched for anti-mod, etc.)
There are some guides floating around out there that will explain all this--dig around a bit. If you find one by Charlie or Balto....you can pretty much take it as law.