Once you have patched a game and burned it to a blank CD'R you don't need to patch it again when you try and copy it again.

You should be able to make a straight copy using either CloneCD or CDRwin.

One question thats comes to mind is have you in any way damaged the original back-up as this could be causing a corrupt image being created.

You could check your images before burning then back to CD is use CDmage and this will tell you if it damaged for not.