Before you spend much more time in Perl, can you get this program to work quietly from the shell? I can't see why your program would interpret '2>&1' or '|' as arguments, or why you get the 'ambiguous redirect' error. Are you sure that your Perl is using a standard (i.e. non-csh) shell? Perl should call something like '/bin/sh -c', which should then eat the redirection characters.

I'd try to run this program from the shell first, and then use the same command line for perl's system command (assuming you don't have to feed the program anything via a pipe or something). If that fails, perhaps Perl is using the wrong shell.

If the program is doing something dumb like talking to /dev/tty, you might have to use something more industrial-strength to talk to this program, like using /dev/pty*, etc.