From your code it seems to be printing back what you initially matched against and only want to print stuff unless it matches a certain $obj_name and $location.

So here is my take on the problem:

use strict;
use warnings;

my $location = "1";
my $obj_name = "Stock3of1";


{

   local $/ = "\n\n";

   while ( <DATA> )
   {
     if ( /<\?--([^-]*)-([^-]*)-->(.*?)<\/\?--([^-]*)-([^-]*)-->/s )
     {
       print unless ( $location eq $1 and $obj_name eq $2);
     }
   }

}

__DATA__
<?--1-News1-->
<b>This is option News 1 of 1</b>
</?--1-News1-->

<?--1-Weather2of1-->
<b>This is option Weather 2 of 1</b>
</?--1-Weather2of1-->

<?--1-Stock3of1-->
<b>This is option Stock 3 of 1</b>
</?--1-Stock3of1-->

<?--2-Second1of2-->
<b>Option Second 1 of 2</b>
</?--2-Second1of2-->

<?--3-Third1of3-->
<b>Option Third 1 of 3</b>
</?--3-Third1of3-->
[download]

I believe this does what you wanted.

-Enlil