Quick update Jet, just managed to copy a cd based ps2 game no problems (crash bandicoot, wrath of cortex) but still having no luck regarding dvd-rom based ps2 games. All i did was read it as an image file then write it from the image file using
clone cd, tool about 5 mins. Used the cd swap magic boot disc, then swopped it over for the copy disc and it has loaded up fine and is working as well as the original.