print "@firstLine1\n";
print "@firstLine2\n";

##</code><code>##

open my $fileText, '<', $file or die("Error opening \"$ARGV[0]\": $! ");

my @firstLine1;
my $count = 0;
while(<$fileText>){
    chomp;
    if($count++ == 0){ # I will eventually read the whole file...
        @firstLine1 = split(/\t/);
        last;
    }
}

open my $fileText2, '<', $ARGV[1] or die("Error opening \"$ARGV[1]\": $! ");
my @firstLine2;
$count = 0;
while(<$fileText2>){
    chomp;
    if($count++ == 0){ # I will eventually read the whole file...
        @firstLine2 = split(/\t/);
        last;
    }
}

print "@firstLine1\n"; # All values print fine!
print "@firstLine2\n"; # All values print fine!

foreach my $sample1 (@firstLine1){
    foreach my $sample2 (@firstLine2){

        # I get some strange output here.
        # Everything will print fine -> 
        # $sample1: <sample1_value> $sample2: <sample2_value>
        # until the last value in the array, 
        # everything gets messed up -> 
        # sample1:$sample2: <sample2_value>

        print "\$sample1: \"$sample1\"\t\$sample2: \"$sample2\"\n";
    }

        # If I try a compare, it fails
        if($sample1 eq $sample2){
            # doesn't get here on the last value.
        }
}