Hello RichyD
The ticketing system is not automatically taking your Swiss Half Fare Card into account. This works with the yearly Half Fare Card for residents only, while the Swiss Half Fare Card is jissued like a ticket - you have to show it to the conductor at every ticket check.
To activate the half fare reduction for the Swiss Half Fare Card, you have to do it manually. When you book tickets via the website, hit the “Process passengers | reductions” button.
Then, select the Half Fare Card from the possible reductions. When you are logged in as a user, the setting is preserved for the next purchase.
Kind regards,
Roland