You don't get the extra roll on the Run move.
Every time the stormboyz unit utilises its rokkit packs to move or fall back roll a d6.
If you check the rules for Jump Infantry, they only actually use their jump packs (or whatever the army in question's equivalent happens to be) in the Movement phase, and when Falling Back.
So the Run is not a movement in which the Boyz 'utilise their rokkit packs' ... and so they don't roll.