Here are a few pointers to get you on your way:

• use strict; use warnings
• Assign values to a hash like this: my %hash = ( key1 => 'val1', key2 => 'val2' );
• Indent your code - try using perltidy or similar to do this.
• Don't try to pack too much login into one line: for example:

  $MissingPatchList{$BulletinID} = "$pad{(length($MissingPatchList{$Bull
  +etinID}))}$MissingPatchList{$BulletinID}";
  
  # better written as:
  
  $MissingPatchList{$BulletinID} =
      $pad{ length( $MissingPatchList{$BulletinID} ) }  
      . $MissingPatchList{$BulletinID};
  [download]

• Comments: a few comments serve both to make the code make sense and to break up the flow into nice chunks.
• This code could (I think) be broken down into subfunctions. This would make it easier to test. You are testing arn't you?

The whole XP programming thing would love this task. The XP way would be to write a load of tests so that you know the code works and then to start changing the code - testing as you go. As long as the test still work then the code is good.

You might like this article: http://www.perl.com/pub/a/2003/10/09/refactoring.html.