If I choose one option, I can click buy now which adds it to the cart. The Buy now button then changes to a Checkout button.
This is fine unless I decide I want to add another option to the cart. If I select a second option and click the button, it just takes me to the cart without adding the new choice.
I tried to change to the default theme and reproduce your issue, I found maybe this issue is EDD bug, it’s nothing to do with the theme. I will send feedback to EDD support team.