Did you unlearn your skills at the trainer? If so you have to reassign your dragon skills, as well (ie the only skills that would show up would be the ones from equipment bonuses).
If that isn't the problem, do the skills not show up at all in the menu (assuming you get the item/skill selection menu after holding a D-pad direction down), or are they listed but you can not select them? There shouldn't be any restrictions on assigning skills to the buttons or D-pad directions, except that Firebreath is fixed to the right trigger and can not be changed.
Did you try assigning a skill that you have set for one of the buttons to one of the pad directions?
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