While most character sheets list “flat-footed” as a “separate AC,” it isn’t actually so in game terms: it’s just a common enough circumstance that the people who made the sheet wanted to make sure you’d have it easily available.
(As opposed to “touch AC,” which really is a separate stat that you have.)
So you roll against their AC—whatever that is at the time. If they have the Dodge feat and have chosen you for it, then the DC for your Jump check is 21 higher than it would have been. If they are flat-footed and thus denied their Dexterity and Dodge bonuses to AC, then the DC for your Jump check is that much less, and so on.
(Even if your attack would target touch AC—e.g. with wraithstrike or a brilliant weapon—your Jump DC is still their regular AC, because it says “AC” and not “touch AC.” So their armor, natural armor, and shield bonuses to AC make your Jump check harder, even if they don’t make your attack harder.)