iTunes is becoming worse and worse when grabbing a large number of files from the iPad's documents folder. I think the limit is around 600 files at a time. Try to download any more than that from the iPad to your computer and iTunes locks up. I have reported this bug, but for now, if you need to backup your entire iPad, select groups of files at a time. Just click on the first file and then go down the list a bit and then shift-click to select a group. Then copy those files. Then continue on from the last downloaded file.