My guess is that you're adding empty key/value pairs to the hash. Show us the result of your extra print statements (if there's not too much).

What does trim() do? Could it be responsible for creating empty entries in your hash?

Some other comments about your code:

• You are using strict and warnings, aren't you?
• Perl has the wonderfull keys function which allows you to replace this

  my $count = 0;    
  while (my($key, $value) = each(%ip_discover_count) and $count == 0)
  {
          $count++;
  }
  if ($count > 0)
  [download]

  with this:

  if ( keys %ip_discover_count )
  [download]

• Always check that open succeeds: open (SEED,">$dir/$seedFileName") or die $!;
• "$CC\_discover.txt" doesn't do what you think it does. Use single quotes, or double up the backslash.

update: keys is unnecessary, as demonstrated by dave_the_m. I was thrown by the OP's use of $count, which doesn't count.