Your code looks pretty good. I just recoded it a bit. This should be ok on either Windows or Unix(the chomp() gets rid of whatever line terminator is there and the way I parsed the 2nd file throws that away too. Maybe you have some non-printing garbage in there? Or your "real thing" is a bit different from this example? 
#!/usr/bin/perl -w
use strict;

die "Usage fileReference File2Check >outfile" if @ARGV != 2;
my ($fileRef, $file2Check) = @ARGV;
open (REF, "<$fileRef")    || die "unable to open $fileRef";
open (CHK, "<$file2Check") || die "unable to open $file2Check";

my %seen = map{chomp; $_ => 1 }(<REF>);

print grep { my $token = (split /,/,$_)[0];
             !$seen{$token}
           }(<CHK>);

__END__
fileref:
ab
gh
kl
mn
op

file2check:
ab, 1234
cd, 2343
ef, 1253
gh, 4543
ij, 2343
kl, 2453
mn, 4753

output:
cd, 2343
ef, 1253
ij, 2343

[download]

In reply to Re: list lines not found in config (while+if) by Marshall
in thread list lines not found in config (while+if) by tangledupinperl

Title:
Use:  <p> text here (a paragraph) </p>
and:  <code> code here </code>
to format your post, it's "PerlMonks-approved HTML":


  • Posts are HTML formatted. Put <p> </p> tags around your paragraphs. Put <code> </code> tags around your code and data!
  • Titles consisting of a single word are discouraged, and in most cases are disallowed outright.
  • Read Where should I post X? if you're not absolutely sure you're posting in the right place.
  • Please read these before you post! —
  • Posts may use any of the Perl Monks Approved HTML tags:
    a, abbr, b, big, blockquote, br, caption, center, col, colgroup, dd, del, details, div, dl, dt, em, font, h1, h2, h3, h4, h5, h6, hr, i, ins, li, ol, p, pre, readmore, small, span, spoiler, strike, strong, sub, summary, sup, table, tbody, td, tfoot, th, thead, tr, tt, u, ul, wbr
  • You may need to use entities for some characters, as follows. (Exception: Within code tags, you can put the characters literally.)
            For:     Use:
    & &amp;
    < &lt;
    > &gt;
    [ &#91;
    ] &#93;
  • Link using PerlMonks shortcuts! What shortcuts can I use for linking?
  • See Writeup Formatting Tips and other pages linked from there for more info.