Info. below on the use of ID3 tags by the Clip and Clip+, for file organization and display, in case that answers your issue. Also, you might want to look for the files under the Clip+'s folder option under Music, in case you have not done so.
As a general matter, the Clip players internally organize files by “ID3 tags,” metadata put into the files which provides identifying information concerning the files under various categories, typically including artist/author, album/book, selection title, genre and year. The original Clip generally does not organize by folder view, as does your computer. Instead, the ID3 tags are used to create the lists that show up on the Clip’s display. This has become something of the default for modern audio players. The Clip+, in a welcome addition, offers both forms of organization: ID3 tag organization using the ID3 tags (resulting in artist, album and title listings), and a separate folder/file view.
When you rip music from a CD, many rippers offer the option of filling in the ID3 tag fields from free Internet databases. You also can manually enter this information and edit it via tag editors such as MP3Tag and The Godfather (Internet freeware). Windows users can edit it by right clicking on the file and going to one of the screens under Properties. (For more than occasional editing, a tag editor is easiest.)
If your Clip reports many files as Unknown or seems to organize and show file information erratically, it often is because the ID3 tag data is missing or is incorrect or inconsistent. Again, as a general matter, for the album, artist and title listings, the Clip does not care about your folder and file organization or the names selected for them–the ID3 tags control.
Hence, a good reason, when ripping CDs, to enter in the ID3 tag information. With many rippers, this can be done automatically or with the minimum of extra work. At this point, for me, it’s just part of my ripping process, along with adjusting the files’ volume/gain through MP3Gain (also Internet freeware).
Especially for those who have not entered ID3 tag info., various people here and at anythingbutipod.com (the Clip forum) have developed software that will create a playlist for each of your Clip folders. That way, after running the software on your Clip folders and files, you simply play those playlists, each of which will play each of your folders. Here are 3 of the playlist creators to check out.
An exception to the above:
Files put into the Clip’s or Clip+‘s Podcasts or Audiobooks folders, or elsewhere on the Clip but with the Podcast or Audiobook ID3 tag filled in as such, will use the files’ folder and file names for organization. That way, for these more transitory of files, you can avoid having to fill the tag info. in, if you would like, instead relying on the folder and file names.
I hope this helps some–