David,
Under your ‘FTP Options’ tab for the thread, what ‘Dir List’ command do you have specified? I believe the ‘nlst’ command is the default, and would normally list the files in lexicographical (dictionary) order. To double-check the order the list of files is being returned in, you should be able to turn up the EO on the thread and see the information in the log.
Hope this helps.
Jim Cobane
Henry Ford Health