The OP's problem was that he did not know exFAT was very flexible and more flexible than NTFS. He could have copied larger than 4GB single files by reformatting to larger sector sizes. Under Windows 7, he could reformat his 128GB or 64GB USB flash drive to default sector size (384KB/sector instead of generally preformatted 128KB/sector). Windows XP or Vista may need appropriate MS's update to reformat exFAT formatted USB drives to copy larger than 4GB single files.
But I don't know if there is another way to solve that empty folder problem with 64GB or larger USB flash drives.