If you are just using windows to copy the files over, a lot of times if it cannot copy a certain file it will just kill the whole transfer. I have used a free program called teracopy that will let you keep the copy going even if it comes across a bad file. It will also tell you which files were bad so you can try to manually copy them over. Maybe there is a bad file or 2 in your list to be copied that are stopping the whole transfer from completing. You may also want to try breaking it up into smaller groups to see if they will transfer that way.