You seem to have done correct, anyway I want to repeat this whole procedure:
1) Connect the CORTEX to the PC software and power it, so that you get a green bar stating 'connected' in the right bottom screen.
2) Now, in case you did any changes before already, click 'Read all' in the Global page. This ensures that all data from the system is now available in the software too. The green equal sign in the right bottom needs to show up. From any changes on, do not care about the un-equal sign in the Reset window, as this only shows that the unit is not matching the factory state any more.
3) Switch to the Options page, click 'Inverted' (and in case set the orientation for the socket side). Herewith the green equal sign changes to un-equal. Now click 'Write all' right here (no need to change to the Global page again, but does not make a difference), and the equal sign needs to show up again.
That's it and must work. There is no reason why it should not, no setup issue that would affect this parameter not to be written and changed, even on a factory state unit with no teach-in yet (as this needs to be set correct prior to teach-in).

And update the firmware to V.15. Not affecting this special issue either, but highly recommended for best flight performance. Use the update firmware button in the Global page and follow the instructions.