It's not clear if the discrepancies you see are only in the file sizes reported or something else.
When you say that there are "different numbers of folders and files" do you mean that some files and/or folders did not get copied, that some extraneous files and/or folders appeared in the copy destination, or something else?
If you're copying using drag-n-drop, you may get extra copies. This is caused by a shaky hand and/or a too-sensitive mouse.
If you are seeing different file sizes for the same file(s), make sure that you're looking at the actual file size and not the "size on disk." These two numbers are almost always different because Windows allocates disk space using "file allocation units"
or clusters.
In Windows XP, the default file allocation size for partitions larger than 2 GB (which should include almost every hard drive today) is 4KB, but this size can be set to a smaller value when the partition is formatted. If a drive originally was formatted
using the FAT file system and then CONVERTed into NTFS, Windows may have set the file allocation size of the converted partition to only 512 bytes. For more info, seeKB314878 and
Converting FAT32 to NTFS in Windows XP . If the cluster size on the source drive is different from the cluster size on the destination size, the "size on disk" for the same data could well be different.