Remember that PS2 discs are either CD format of DVD format. Sounds like you are trying a DVD format disc with CloneCD - wont work.
For PS2 CD format games CloneCD is still the best burning software.
For PS2 DVD format games you need a DVD burner (pioneer A03/A04) and prassi primo DVD or Nero burning software.
Tutorials at
www.psxcopyworld.co.uk
Hope this helps, any further questions post back.