With Perl 5.8.5, I can't reproduce your error. I've changed your code around a bit to make it work with strict and removed some of the file tests because they are redundant but still:

use strict;

my @files = qw(CaseComment.csv);
my $dir1 = ".";
my $dir2 = ".";

########################
# OPEN THE STEP 1 FILE #
########################
foreach (@files) {
    my $filename = "$dir1/$_";
    #chdir($dir1); # replace by "$dir/$_"
    
    # Redundant - open() will die with
    # an informative message anyway
    ## Verify Files exist
    #die "File: '$filename' does not exist: $!"
    #   unless -e $filename;
    ## Verify Files are read/writable
    #die "File: $filename isn't read or writable \n $!"
    #    unless ((-r $filename ) && (-w $filename ));
    
    ### Open the file
    open (FILE, "<", $filename ) or die "Cannot open the file '$filena
+me': $!\n";
    #select((select(FILE), $/ = undef)[0]); # what is that for?
    
    my @array_contents = <FILE>;
    
    close (FILE) or die $!;

## DO SOME STUFF
##########################
# CREATE THE STEP 2 FILE #
##########################
    #chdir($dir2);
    
    my $contents = <<TESTCOMMENTS;
Line 1
line 2
linE 3
TESTCOMMENTS
    
    my $outputfile = "$dir2/STEP2_" . $_;
    warn "Writing '$contents'";
    open(OUTFILE, ">" , $outputfile) or die "Couldn't create '$outputf
+ile':$!";
    print OUTFILE $contents;
    close OUTFILE or die $!;
};


##########################
# ACCESS THE STEP 2 FILE #
##########################

#chdir($dir2);
my $commentsfile = "$dir2/STEP2_CaseComment.csv";
open (SFCOMMENTS, "<", $commentsfile) or die "Cannot open Salesforce C
+omments file '$commentsfile' : $! \n";
my $count = 0;
while (<SFCOMMENTS>) {
    print "Count is: $count \n";
    $count ++;
}
close SFCOMMENTS or die $!;
[download]

outputs for me:

C:\Projekte>perl -w tmp.pl
Writing 'Line 1
line 2
linE 3
' at tmp.pl line 44.
Count is: 0
Count is: 1
Count is: 2
[download]

Maybe your assignment to $contents is somehow wrong? More debugging information is needed.