AB data

samaccountname,givenname,sn,initials,employeenumber,symphonyemployeety
+pe,mail,title,department,company,l,physicaldeliveryoffice,streetaddre
+ss,st,postalcode,telephonenumber,manager
barsu991,Uttiam,Barski,K,20114598,IKP,William.Barski@pulse.org,Chief o
+f Cooks,Day Kitchen,MILIFO,Alpena,Kitchen of the World,400 Baker,WI,5
+0987,555-555-5555,"cn=manager1,ou=users,ou=Kitchen,dc=Kitchen,dc=net"
walkl003,Larry,Walker,J,,IKP,Larry.Walker@pulse.org,Cook,Day Kitchen,M
+ILIFO,Alpena,Kitchen of the World,400 Baker,WI,50987,555-555-5551,"cn
+=manager1,ou=users,ou=Kitchen,dc=Kitchen,dc=net"
karss001,Steven,Karsten,Y,20146598,IKP,Steven.Karsten@pulse.org,Dishw,
+Day Kitchen,MILIFO,Alpena,Sully's Kitchen,48720 Belcard,IL,34567,,"cn
+=manager1,ou=users,ou=Kitchen,dc=Kitchen,dc=net"
zingk072,Kevin,Zingerman,K,,,Kevin.Zingerman@pulse.org,Baker,Day Kitch
+en,MILIFO,Alpena,Kitchen of the World,205 Willy B. Temple,WI,50987,,p
+eizs194,Samantha,Smith,B,20134743,IKP,Samantha.Smith@pulse.org,"Man, 
+Broiler",Day Kitchen,MILIFO,Alpena,Kitchen of the World,205 Willy B. 
+Temple,WI,50987,,"cn=manager1,ou=users,ou=Kitchen,dc=Kitchen,dc=net"
hutcy231,Yaren,Hutchinson,W,20145712,IKP,Yaren Hutchinson,@pulse.org,B
+ottle Washer,Day Kitchen,MILIFO,Alpena,Kitchen of the World,400 Baker
+,WI,50987,,"cn=manager1,ou=users,ou=Kitchen,dc=Kitchen,dc=net"
haserz221,Zebediah,Hasermann,L,,IKP,Zebediah.Haserman@pulse.org,Purcha
+ser,Day Kitchen,MILIFO,Alpena,Kitchen of the World,400 Baker,WI,50987
+,555-555-5555,"cn=manager1,ou=users,ou=Kitchen,dc=Kitchen,dc=net"
[download]

This solution assumes 'samaccountname' is correct between the 2 files and checks that the headers are the same for each file. Also I noticed there were some entries in the AD file that weren't in the HR file. I didn't try to compare since they weren't in the same file. I didn't know how you would handle this situation.

#!/usr/bin/perl
use strict;
use warnings;

my $hr_file = 'HR.txt';
open my $fh, '<', $hr_file or die $!;

my (undef, @hdr_hr) = split /,/, <$fh>;
chomp @hdr_hr;

my %hr_data;
while (<$fh>) {
    chomp;
    my ($id, @rest) = split /,/;
    @{ $hr_data{$id} }{@hdr_hr} = @rest;
}
close $fh or die $!;

my $ad_file = 'AD.txt';
open $fh, '<', $ad_file or die $!;

my (undef, @hdr_ad) = split /,/, <$fh>;
chomp @hdr_ad;

@hdr_ad ~~ @hdr_hr or die "Uncompatible headers between HR and AD file
+s\n";

my %ad_data;
while (<$fh>) {
    chomp;
    my ($id, @rest) = split /,/;
    @{ $ad_data{$id} }{@hdr_ad} = @rest;
}
close $fh or die $!;

for my $id (sort keys %hr_data) {
    next unless exists $ad_data{$id};
    for my $hdr (@hdr_hr) {
        my $description_hr = $hr_data{$id}{$hdr};
        my $description_ad = $ad_data{$id}{$hdr};
        print "$id,$hdr,$description_hr\n"
            unless $description_hr eq $description_ad;
    }
}
[download]

Output I got is:

barsu991,mail,Uttiam.Barski@pulse.org
barsu991,title,Director of Cooks
haserz221,sn,Haserkrilk
haserz221,employeenumber,20125471
haserz221,mail,Zebediah.Haserkrilk@kit.org
haserz221,telephonenumber,
hutcy231,givenname,Yello
hutcy231,mail,Yello Hutchinson
karss001,givenname,Sovyetk
karss001,mail,Sovyetk.Karsten@pulse.org
karss001,title,Dishwasher
karss001,physicaldeliveryoffice,Kitchen of the World
karss001,streetaddress,205 Willy B. Temple
karss001,st,WI
karss001,postalcode,50987
walkl003,givenname,Lreblemet
walkl003,employeenumber,20178941
walkl003,mail,Lreblemet.Walker@pulse.org
walkl003,title,Head Cook
zingk072,givenname,Kovon
zingk072,employeenumber,20113578
zingk072,symphonyemployeetype,IKP
zingk072,mail,Kovon.Zingerman@pulse.org
zingk072,manager,"cn=manager1
[download]