Problem with pdf-files in iBooks and organizing after sync with iTuneso

I organize my pdf-files in iBooks in separate folders. After sync from iTunes on my pc I normally find the new pdf-files in det folder pdf-files. Then I moved them over to separat new folders. But last time I sync I get all my PDFs in the main folders PDF-files. And when I tried to move them to a separat folder, they get copied, not moved. Have someone experience the same and a solution?