Itunes U Files No Longer Appearing in the Device in Itunes

Question

I've been using Itunes U files with no problem for a while now but just yesterday something changed. Before I'd drag them into my device like any other file and they would appear in the "music" subfolder of my device. Fair enough. I could listen to them and delete them from there when done.
Now they don't appear anywhere in my itunes. That is, I can put them in my device and listen to them there, but as they don't appear in the music folder anymore (or the podcast folder... or in their own) I cannot delete them. This wouldn't be a problem if I had a big player - but I intentionally have a small player (First Generation 1 GB Nano) so that I limit my options and force my listening behavior.
My only present work around is restoring them to the factory settings. It's kind of a pain to do every other day as you can imagine but what's a boy to do? So... what's going on? A new bug? Some new thing I've missed? Help!!!!!

Answer 1

I have my entire music collection ripped using iTunes and stored on a Mac mini running Windows. It is all in Apple Lossless format and shared with Windows Media Player and Media Center which can play the Apple Lossless files thanks to a solution I came up with along with assistance from Milenko Mitrovic.
While I do deliberately chose to embed 600x600 pixel artwork in each track (disk space is cheap), I also put a folder.jpg of the same artwork in each album folder for the benefit of WMP and Media Center.
The steps I use to do this are as follows.
1. Rip the CD using iTunes
2. Tell iTunes to download album artwork for that Album. Life is made much easier if you only do one album at a time.
3. Look in your Music folder for the iTunes folder and look in that for the Album Artwork folder
4. In the Album Artwork folder will be a Download folder and in that various subfolders eventually leading to a file called something like A392573AD3DE300C-45855BDAB6F38792.itc2 by checking the file creation date/time you will be able to confirm it corresponds with the one you just downloaded.
5. Use the free utility bitmaprip available here http://mark0.net/soft-bitmaprip-e.html to 'extract' the real artwork from inside Apple's proprietary itc2 file. You can then move this to the iTunes album folder for that album and name it folder.jpg
If you then like I do, want to make this artwork embedded, then do the following extra steps.
6. Select one of the tracks for the album
7. Copy the artwork to the clipboard
8. Clear the downloaded artwork
9. Delete any folders left in your Album Artwork folder so they do not confuse you for the next album
10. Select all the tracks for the album
11. Paste the artwork in