Hi Adam,
If I understand how you are using the RC-1216H correct, then it seems you are mixing up the different types of virtual Com ports that exists
The Com port which is added to the PC when you connect the RC-1216H via USB is not related to the Com port that is created from inside the Setup Manager program. The USB Com port is not needed if you want to use the remote Com/serial port feature of the RC-1216H as the Com port created by the Setup Manager is a software only port.
So in your case it's most likely the drivers for the software only/remote com port which do not work after you upgraded to Win10. To fix your problem it might help by installing the latest Setup Manager found here:
http://www.webswitch.se/wp/?page_id=190as it installs new drivers too. You might have to manually uninstall the previous version first. In case it still does not work you can follow this FAQ article as it applies to those com ports too:
http://www.remoterig.com/wp/?page_id=3200and do this:
Uninstall all Microbit ports/devices. Answer ‘U’ on the question ‘Do you want to uninstall all Microbit devices automatically?’ followed by ‘C’ to do that. It is advised to unplug all Microbit devices before uninstalling all Microbit devices.
after doing that you have to install Setup Manager again.