In folder view, the Clip Sport simply reads the FAT file system and lists all files in the order they where added to the device by your computer (which usually is alphabetically). No internal sorting is applied. If you later add new content to an existing directory it will be appended at the end of the list.
It is however possible to rearrange the content with third-party software like FAT Sorter (Windows) or FATSort (OS X, Linux) if needed.