I think the .iss file given with the sources are not having complete information for silent installatio of the application. Create your own .iss file and try, below steps can be followed
a) create response file for ur setup.exe using -r switch. This will create setup.iss under c:\windows folder. Similarly uninstall can be also recorded. (In both the cases setup.iss will be created, rename the same as per your requirment)
b) Use setup.iss file for silent installation using /s /f1<path of .iss file>
    There shouldn't be any space between f1and path of .iss file.

Refer InstallShield section on http://unattended.sourceforge.net/installers.php for further information.

If Yankiar's suggestion does not help solve this, it is highly likely that the Installshield install has a custom dialog or other vendor-specific content, that is not handled by the normal iss response file process.
However, as this is a Wise forum and not an Installshield forum, you may find that posting in the forums at Installsite.org or on the Acresso forums may give you a more detailed solution as those ARE the correct places to ask Installshield questions.

I was lucky with 2 of the setups using Yankiars suggestion,  for the others it did not work probably caused by the reason that Edt gave.
It is best to post this on an installshield forum probably.