Leo says that ever since the iPad got wireless sync, he stopped using iTunes for it. Frankly, iTunes for Windows is a "bag of hurt," and just doesn't work right. He could try and reinstall iTunes, as some in the chatroom think that'll restore the capability to save to folders.
Using DropBox is an easier idea, and it's free. iCloud is still the easiest, however. The chatroom has found an Apple technote that will help Gary sync specified folders. Check it out here.