Sounds like if you've used the correct settings for clonecd , that you reader/re-writer does not read sub-channel data(which is a part of standard psx/libcrypt protection).
Goto
www.elaborate-bytes.com (cdclone website) and check if you reader and writer are supported.If so then try using your re-writer to read and write the disc (keep you read speed down to 8x max and write speed to 4x).
Better still goto
www.cnet.com and download clony xxl protection detection program ,it will detect the protection on the disc(not just psx either) and pass on the parameters to clone when you start it up through this proggy.
Just as a after thought,I know that FF9 uk/pal and american version have extra mod-chip protection ,they have to be patched with cdrwin or fireburner.
A good tutorial is avilable on megagames .