1) how large are your input files (in lines)?
Ans : 13000 lines

What OS are you running on?
Ans : Sun Solaris and Linux

Are your input files always the same length (in lines)? With only some words changed? Or with whole new lines added?
Ans: The number of inputs lines and their contents vary depends on platform.

#!/usr/bin/perl

# http://perlmonks.org/?node_id=1140982

use strict;
use warnings;

my $filenameone = '1.pc.d'; # change to your main filename
my $filenametwo = '2.pc.d'; # change to your secondary filename

my @parents;

# should work on linux, not sure what Solaris diff args are...

open my $fh, '-|', "diff -U 999 $filenametwo $filenameone" or die $!;
scalar <$fh>; # ignore first
scalar <$fh>; # two lines

while(<$fh>)
  {
  s/^([ +])(?=( *))// or next;
  $#parents = length($2) - 1; # truncate array
  push @parents, $_;
  $1 eq ' ' and next;
  defined and print, $_ = undef for @parents;
  }
[download]

If this doesn't work, please give a small test case that shows the failure.

Thanks a lot Anonymous Monk.
This works awesomely on my cofig files of lines 12500 each and gives output in no time.
Apart from testing for regular differences ,I tried inserting a blank line in the config file, and it worked there too.
Thanks once again. :)