OK, I have figured out what is happenning, so I will post it here in case someone else has the same issue.
The gap that appears over my new theme’s design, I discovered, only appears when I am logged-in. So this is the space that WordPress uses to display it’s buttons for managing the site. It just so happens that I must have disabled this unknowingly.
I don’t know how to re-enable this, but it is not that important since I don’t need those buttons, I just edit from the dashboard and this only happens if you are logged in.