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Es una restricción de seguridad, tu aplicación la tienes que poner en un subfolder llamado fscommand.
In Macromedia Flash MX the external application must be in a subfolder named 'fscommand'. This subfolder must be in the same directory as the projector which uses the fscommand action. This security restriction helps prevent malicious use of the exec option.
The following script launches the Windows application someApplication.exe, which is in the fscommand folder on the same level as the projector:
on (release) {
fscommand ("exec", "someApplication.exe");
}