There is an extra character "\n" at the end of the line, this becomes the final element of the array. Change sub count_fields such that my @x = split( /\t+/, $line); to see what I mean. The fact that there are empty elements on the way to the last legitimate element is of no interest, try the following with and without the + modifier on \t in the split.

#!/usr/bin/perl

use strict;
use warnings;

my $line ="A\tB\tC\tD\t\t\t\t\n";

print "Test string line: $line";

print "Split without chomp: ";
my @x=count_fields( $line );
check_for_null_elements(@x);

print "Split _after_ chomp: ";
chomp $line;
@x=count_fields( $line );
check_for_null_elements(@x);

exit;

sub check_for_null_elements {
   foreach my $element (@_){
      print "Empty element found\n" if ($element eq "");
   }
}

sub count_fields {
   my ($line) = shift;
   my @x = split( /\t+/, $line);
   my $count = @x;
   print "$count fields.\n";
   return (@x);
}
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