Do the personal experiences of qualia, such as what it is like to smell a flower, bring about issues for functionalism?
Yes, qualia very much pose a problem for functionalism -- that is what they were articulated to point out. Mary can functionally do vision science, but EXPERIENCING vision adds something to her consciousness that functionalism does not capture at all. Also, explicitly 99% of human mental processing is unconscious -- IE it has no qualia, but that processing is FUNCTIONAL. Once more -- function =/= consciousness.
Chalmers Zombie thought problem also notes zombies can do functions, but don't have qualia, and that the experiences of qualia is what makes us conscious.