I think that maybe the problem comes from the assignment in the child @ftpDirectoryListing = @deDuppedArray, but you haven't actually called pollDaemonParent($user) yet, which assigns to @deDuppedArray. I would guess that maybe if you changed main to a different order it might solve this :

pollDaemonParent($user); ## assign to @deDuppedArray
my $startingInstanceNum=1;
my @kids;
for (1 .. $maxStripeInstance)
{

    $stripeInstance = $startingInstanceNum;
    unless ($child = fork)
    {        # i'm the child
        die "cannot fork: $!" unless defined $child;
        pollDaemonChild($user); ## read from @deDuppedArray
        exit;
    }

    push @kids, $child;  # in case we care about their pids
    $startingInstanceNum++;
}
print "@kids\n";
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I can't actually test this though... so i could be very wrong. HTH.