Did you purchase the all in one collection or just the SoA expansion? The all in one Ultimate Seekers collection will start an FFXI isntallation wizard, then present you with a list of stuff to install - POL, base FFXI, game, DirectX 8.1, and all the expansion. Just check Seekers if that's the only thing you need to install.
If it's just the single expansion, make sure you're trying to install it in your actual FFXI directory. You may have installed it in an unusual place the first time, and if it can't detect it in its default location, it will be confused and say you have to install the whole thing.