This can be caused by treating the "Add Milestone Detail to Autoresponder HTML" as the original Autoresponder.

If you have added content (with a signature) in this section:
  1. Fundraising -> Teamraiser
  2. Step 7: Manage Milestones
  3. Step C: Add Milestone Detail to Autoresponder HTML
  4. If there is a signature there, it will like duplicate as the ACTUAL Autoresponder is located here:
  1. Fundraising -> Teamraiser
  2. Step 10: Manage Autoresponders
  3. Edit the Autoresponder: "Congratulations for Reaching a Fundraising Milestone"
  4. If there is a signature there as well, then that is why there are two signatures (or any duplicate content located in both of these sections)
The main issue is that the first section is additional content to the actual autoresponder, not a separate one.