You need to surround all the filenames with quotes. The shell will otherwise execute whatever is before the first space. Try something like this:
Dim filePathArg As String = """C:\Documents and Settings\Administrator\Desktop\MSI Installer\Dependency Setup\SQL Setup\x86\setup\setupsql.exe"" -s -fl ""C:\Documents and Settings\Administrator\Desktop\MSI Installer\Dependency Setup\SQL Setup\Unattended File\setup.iss"""
Good luck!