To add to moritz suggestion of a hash above, couldn't you do the whole thing in just one script? You don't need to sort if you use a hash so it becomes much simplier.

For example:

#!/usr/bin/perl

use strict;
use warnings;

my %dup;
while (<DATA>) {
    my @tmp = split /,/;
    if (exists($dup{$tmp[6]}{$tmp[4]})) {
        print "DUPLICATE!\n  Device: $tmp[6]\n  Policy: $tmp[4]\n\n"
    } else {
        $dup{$tmp[6]}{$tmp[4]} = 1
    }
}

__DATA__
4778228,0,0,,Policy_name1,Incremental,Device_name1, ,1291910125,000000
+0053,0000000000, ,1 ,,,,,0,,root,0,13,1,99998,root,x,1,30,0,0,0,0,0,4
+778228,,,,,,,,,,,,,0,0,1,0,0,,0,,,,Max
4778228,0,0,,Policy_name2,Incremental,Device_name2, ,1291910125,000000
+0053,0000000000, ,1 ,,,,,0,,root,0,13,1,99998,root,x,1,30,0,0,0,0,0,4
+778228,,,,,,,,,,,,,0,0,1,0,0,,0,,,,Max
4778228,0,0,,Policy_name3,Incremental,Device_name3, ,1291910125,000000
+0053,0000000000, ,1 ,,,,,0,,root,0,13,1,99998,root,x,1,30,0,0,0,0,0,4
+778228,,,,,,,,,,,,,0,0,1,0,0,,0,,,,Max
4778228,0,0,,Policy_name2,Incremental,Device_name2, ,1291910125,000000
+0053,0000000000, ,1 ,,,,,0,,root,0,13,1,99998,root,x,1,30,0,0,0,0,0,4
+778228,,,,,,,,,,,,,0,0,1,0,0,,0,,,,Max
[download]

Output:

C:\> test.pl
DUPLICATE!
  Device: Device_name2
  Policy: Policy_name2
[download]