Make sure you use warnings and strict. Make sure you check to see if the call to open2 failed.

open2 (*BOY, *FLY, "$flyprog -q") || die "open2 $flyprog - $!\n';
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Does fly.exe stream the data back to you via STDOUT? If so you might want to loop over the STDOUT filehandle:

while (<BOY>) {
   $output .= $_;
}
close (BOY);
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-- vek --