When you say 'active', do you mean you have at least one level in all seven skills?
Which skills show up in the skill menu when assigning button functions, and which (besides Firebreath) have at least 1 level (from your own skill points or equipment bonuses) but do not appear?
If you pause the game and hit a shoulder button, it brings up a menu similar to assigning button functions. Do just the same 3 skills show up there, as well?