Does a rogue with Uncanny Dodge is still flat-footed when failing an Acrobatic check to move through a threatened area or those the passage that says "using Acrobatics in this way, you are considered flat-footed and lose your Dexterity bonus to your AC (if any)" only applies to the moving on "narrow surfaces and uneven ground without falling" bit.
(Uncanny Dodge says she can't be caught flat-footed.)