Your common XP to 7 PC uses NTFS and most sticks are FAT32. This can lead to exactly the issue you noted.
You can also use a better app to copy files and folders. I'll give a link after my first name.
I'm having an odd problem with a new Toshiba flash drive. I have two PC's, one running XP (for downloading) and one running Windows 7 (main PC).
I've formatted it in XP, and let both systems recognize the drive.
In both 7 and XP, the flash drive does all kinds of strange things. It's not copying some of the files, but it lists as being filled to capacity. In one case, it listed as having 38 GB of data, on a 32 GB capacity drive. In some cases, it apparently stops copying halfway through, but shows all the folders anyway.
Any help or suggestions are appreciated.