I've extracted the "Paquet Builder - Advanced Self-Extracting Zip Archive" installer for Clone CD v4.4.3.1 into the following folder:

CD ROOT\$OEM$\Install\Applications\Clone

I have made as answer file with "Setup.exe /r /f1c:\clone.iss"
I renamed the clone.iss answer file to setup.iss and dropped it into the Clone directory where the setup.exe is.

I then added the following to my apps.cmd RunOnce install file:

REG ADD %KEY%\040 /VE /D "Installing Clone CD 4" /f
REG ADD %KEY%\040 /V 1 /D "%systemdrive%\Install\Applications\Clone\Setup.exe -S -sms" /f
REG ADD %KEY%\040 /V 2 /D "REGEDIT /S %systemdrive%\Install\Applications\Clone\register.reg"

If I run this install command as listed above in Windows, it looks like it silent installs (nothing comes up on screen) but it doesn't actually install anything...
If I run the installer normally without any silent switches, the first thing it brings up is an error saying that I am located in United States and amplify weak sectors will be disabled (like it did when I made my answer file)... maybe this has something to do with it? But I am not located in United States all my windows settings are set to Australia?

think you may have made a typo, the current version is 4.3.2.2 not 4.4.3.1.

not sure how to fix your problem though.

maybe that is my problem... the version i have got is probably too old and maybe uses different instructions than the 4.3 version (these are the instrutions i used)

I just downloaded the lastest version (the one you mentioned) and also I found another topic regarding silent install of Clone CD which has a link to an AutoIT script and .EXE to auto install Clone silently... hopefully it works.... CloneCD is the only program on my entire cd that doesnt install automatically