I'd check the weblogs, maybe you'll find a bit more info in there. I do also suspect permissions issues but then again I've seen weirder things....
you can also try running it this way... 

$output=`/opt/csw/bin/octave -qfH < $filename`;

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In reply to Re: Running Command Line Programs from a CGI Script by cool_jr256
in thread Running Command Line Programs from a CGI Script by maslofer

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