Long list of remarks follows...

for my $arg (@ARGV) {
    #$script=$ARGV[0];
    #$stanza=$ARGV[1];
    $metricsfile=$ARGV[0];
    $resultfile=$ARGV[1];
    }
[download]

The for loop does nothing, remove it!

use strict;   # always!
use warnings; # always!
[download]

### Assigning the argument file to in_file ####
$in_file = $metricsfile;
[download]

No need for cmts that do not improve readability, and even degrade it. Well written code should be self explanatory.

Why assigning to yet another scalar and not using $metricsfile directly?

open (IN, "<$in_file") or die "Can't open $in_file: $!";
[download]

For the n-th time, n being a huge integer: you'd better use the 3-args form of open and lexical filehandles.

### A while condition to read all the lines in a file and place in an 
+array####
#my $linenum=1;

while(@linesFromMetrics=<IN>){ # opening while loop
[download]

NO! you either want

my @lines=<IN>;
# or
while (my $line=<IN>) { # ...
[download]

 #print "Reading metrics file \n";
 #print $linenum++;
[download]

You may be interested in $. - read more about in perldoc perlvar.

 ### Assigning the argument file to in_file ####
 $input_file = $resultfile;
[download]

Your comment is not consistent with your code in two ways: missing sigil and wrong variable name. One more reason not to have useless comments: if you change, say, a variable name, then you'll have to change the comment as well.

Well, that's kinda too much. I'll suggest you another way round - this assumes your files are reasonably sized:

#!/usr/bin/perl

use strict;
use warnings;

die "Usage: $0 <file1> <file2>\n" unless @ARGV==2;

my %orig=map {$_ => 1} do {
    open my $fh, '<', $ARGV[0] or die $!;
    <$fh>;
};

open my $fh, '<', $ARGV[1] or die $!;
$orig{$_} and print while <$fh>;
 
__END__
[download]

This is intendedly minimal: expand and adapt to your needs!

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

my  $metricsfile = $ARGV[0];
my  $resultfile  = $ARGV[1];

print "MetricsFilename:$metricsfile\n";
print "ResultsFilename:$resultfile\n\n";

my %results;

### Opening the result file to read ####
open( IN, "<$resultfile" ) or die "Can't open $resultfile: $!";

while ( <IN> ) {    
  chomp; # remove newline
  $result{$_}++; # put line into hash as key
}
close IN;


### Opening the metrics file to read ####
open( IN, "<$metricsfile" ) or die "Can't open $metricsfile: $!";

while ( <IN> ) {
  chomp; # remove newline
  if ($result{$_}) {
    print "$_ is in $resultfile\n";
  }
  else {
    print "$_ is NOT in $resultfile\n";
  }
}
close IN;
[download]

First off, your "records" can match without the physical lines matching. For example, the following lines are a record match:

field 1,field 2
"field 1","field 2"
[download]

Given that, what you have to do is adequately parse the CSV files into some kind of records format that's easy to compare. You could do this in memory with data structures, but that will cause problems if your CSV files grow to sufficient size. Better to use a lightwieght database.

I recommend Text::CSV_XS for parsing the CSV, and DBI with the DBD::SQLite2 driver for a lightweight database system.

Some concept (e.g. untested, but conceptually sound) code:

use strict; use warnings;

use DBI;
use Text::CSV_XS;
use IO::File;

my ($file1,$file2) = @ARGV[0..1]; # two first args are files to compar
+e

# create a session filename
my $dbfile = \"Session";
{
  my $sid = "$dbfile";              #stringify ref
  $sid = $1 if m/^SCALAR\((.*?)\)/; #remove all but address
  $dbfile = "$sid.db";
}

#prepare to read files
my $csv = Text::CSV_XS->new();
my $io1 = IO::File->new($file1,'<') or die ("Can't open $file1 for rea
+d: $!");
my $io2 = IO::File->new($file2,'<') or die ("Can't open $file2 for rea
+d: $!");
my $out = IO::File->new("$dbfile.csv",'>') or die ("Can't write outfil
+e: $!");

#init DB connection
my $dbh = DBI->connect("dbi:SQLite2:dbname=$dbfile",'','',{RaiseError 
+=>1});

# Now, read file1 into the DB.
print STDERR "loading $file1 into database...\n";

#-> first line of CSV is header row
my $head1 = $csv->getline($io1);

# create table
$dbh->do(
  'CREATE TABLE file ('.join(' TEXT,',@$head1).' TEXT)'
);

# load db
{
  my $sth = $dbh->prepare(
    'INSERT INTO file ('.join(',',@$head1).
    ') VALUES ('.join(',',map {'?'} @$head1).')'
  );
  until ($io1->eof) {
    my $row = $csv->getline($io1);
    $sth->execute(@$row);
  }
}

# ok, now compare file2 with what's in the DB.
print STDERR "Beginning comparison.\n";

# assuming same header row
$csv->getline($io2);

{
  my $sth = $dbh->prepare(
    'SELECT '.join(',',@$head1).' FROM file WHERE '.
    join(' AND ',map { "$_ = ?" } @$head1).
    ' LIMIT 1'
  );
  until ($io2->eof) {
    my $row = $csv->getline($io2);
    $sth->execute(@$row);
    my $result = $sth->fetchrow_arrayref;
    if (defined $result && @$result) {
      print STDERR '+';
      $csv->print($out,$row); #save matches to CSV
    }
    else {
      print STDERR '-';
    }
  }
  print STDERR "\ndone.\n";
}

print STDERR "Results saved to $dbfile.csv";

# clean up.
$dbh->disconnect();
unlink($dbfile);
[download]