[cloayza]

Según la ayuda de InnoSetup, deberia ser así:

compil32 /cc "c:\isetup\samples\my script.iss"

Algo mas de información:

•Scripts can also be compiled by the Setup Compiler from the command line. Command line usage is as follows:

compil32 /cc <script name>

Example:
compil32 /cc "c:\isetup\samples\my script.iss"
As shown in the example above, filenames that include spaces must be enclosed in quotes.

Running the Setup Compiler from the command line does not suppress the normal progress display or any error messages. The Setup Compiler will return an exit code of 0 if the compile was successful, 1 if the command line parameters were invalid, or 2 if the compile failed.

•Alternatively, you can compile scripts using the console-mode compiler, ISCC.exe. Command line usage is as follows:

iscc [options] <script name>

Or to read from standard input:

iscc [options] -

Example:
iscc "c:\isetup\samples\my script.iss"
As shown in the example above, filenames that include spaces must be enclosed in quotes.

Valid options are: "/O" to specify an output path (overriding any OutputDir setting in the script), "/F" to specify an output filename (overriding any OutputBaseFilename setting in the script), "/S" to specify a Sign Tool, "/Q" for quiet compile (print only error messages), and "/?" to show a help screen.

Example:
iscc /Q /O"My Output" /F"MyProgram-1.0" /Sbyparam=$p "c:\isetup\samples\my script.iss"
ISCC will return an exit code of 0 if the compile was successful, 1 if the command line parameters were invalid or an internal error occurred, or 2 if the compile failed.

•The Setup Script Wizard can be started from the command line. Command line usage is as follows:

compil32 /wizard <wizard name> <script name>

Example:
compil32 /wizard "MyProg Script Wizard" "c:\temp.iss"
As shown in the example above, wizard names and filenames that include spaces must be enclosed in quotes.

Running the wizard from the command line does not suppress any error messages. The Setup Script Wizard will return an exit code of 0 if there was no error and additionally it will save the generated script file to the specified filename, 1 if the command line parameters were invalid, or 2 if the generated script file could not be saved. If the user cancelled the Setup Script Wizard, an exit code of 0 is returned and no script file is saved.

Saludos