You don't have any souls stored away from before you downloaded Dragonborn? Or did you start a new character specifically for it? Because as far as I know. If you activate the plot point in Dragonborn to where Miraak will show up and steal dragon souls, he will continue to do so throughout the main questline for Dragonborn.....im not sure what you should do :-/. I think however I have been able to devour one or two dragon souls specifically to unlock these shouts at certain points. and Miraak didn't show up. Wish I could be more of a help to you.