This is because the perl CGI script on your web server is run by mod_perl module, not perl. There is a specific method for starting a new process in apache CGI, which would look somewhat like the following:

use Apache::SubProcess ();
$command = "C:\\Windows\\iexplorer.exe";
Apache::SubProcess::spawn_proc_prog(undef, $command);

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In reply to Re: system() or exec() in CGI scripts by Roger
in thread system() or exec() in CGI scripts by LupoX

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