You have some logic errors. ie every time through the loop you are resetting the content of @cmd_output. Try this:

my $cs = Net::Telnet::Cisco->new(Host => '123.123.123.123');
$cs->login('login', 'password');

my $DEBUG = 1;

open( FI, $ciscomm_conf ) || die $!;

my( @oks, @fails);

while(<FI>) {
    # remove newline
    chomp;
    # skip blank or comment lines
  next if m/^\s*#/ or m/^\s*$/;
    my $cmd = $_;
    $DEBUG && print "Sending $cmd\n";
    my @cmd_output = $cs->cmd( String => $cmd,Timeout =>60 );
    if ( @cmd_output ) {
        $DEBUG && print "Recv: @cmd_output\n";
        push @oks, [ $cmd, \@cmd_output ];
    }
    else {
        $DEBUG && print "ERR: " . $cs->errmsg . "\n";
        push @fails, [ $cmd, $cs->errmsg ];
    }
}
close FI;
$cs->close;

use Data::Dumper;
print "OK\n", Dumper(\@oks);
print "Fail\n", Dumper(\@fails);
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