I did some more testing and I appear to have fixed the issue, looks like my session file was corrupted.
Try the following to see if helps. This will reset all of the NC1 IO settings in the system back to default, so make sure you know what you need to setup again for each input.
1. Quit the NC1 IO software
2. Open an Explorer Window
3. In the path bar, type %localappdata% (with the %), this will take you to the following location 'C:\Users\NC1-IO\AppData\Local\'
4. Open the 'NewTek' folder
5. Delete (or backup/move/rename) the folder called 'NewTek Connect 1'
6. Start NC1 IO software.
Since I have cleared and reset the session, the SDI output have automatically been active everytime I start the software.