When copying a cd32 cd, try to stick to the ones without audio tracks first, to narrow things down. If you have a cd burner, use that drive to read the discs, as they usually do a better job than dvd or regular cd drives.
Bin + Cue format is probably the best way to go for cd32 cds (custom formats like cdi, img, and nrg are not widely supported, and iso is almost too generic in that it's used by a lot of burning programs that only copy the directory contents when making an image). If CDR-win is making bad images, then either the source cd is bad, your cd-drive is bad, you need an ASPI layer installed, or its something else I can't think of. Good luck!