Hi Carl Farrington,
I'm really sorry that delayed of this reply and I believe my colleague misunderstanding with your issues earlier, I have consult with my colleague regarding this and tested in locally everything is work fine without auto remove the admin component drop down menu item.
Can I have a chance to help you check on this issues again? because it could be something else causing this.
If you could give us a chance again, is it possible using your Akeeba backup with your current data first?
So that I can try install the Komento in your site and replicate on this issues? In case anything happen, we can re-roll back to previous data.
Looking forward of your response.