My Google-Fu is failing me on this one, so I thought I'd toss it to the crowd:
I have a Zune HD 16 Gig along with the standard Zune Marketplace Software, and I am having a serious issue getting all my MP3's to show up in the library. I've directed the software to the top folder where I hold all my files, and it has located and synced most of them, but there's large groups of stragglers that are nowhere to be found. This problem seems more pronounced with audiobooks for some reason. I'm not saying that an entire audiobook will vanish; a few random chapters do show up properly in the library, and when I double-click on the ones that get missed they do in fact play in Zune Marketplace, but if I can't get them on my list I can't get them in my Zune.
I'll give an example just to totally illustrate the circumstances:
Under 'Music' I have a folder named 'Patrick Rothfus - The Name Of The Wind'. When Zune synced this folder, it grabbed '00 The Name of the Wind', '01 The Name of the Wind', '05 The Name of the Wind', '16 The Name of the Wind', etc. 29 out of 92 files. It also put those 29 files into 3 different albums, but that's another matter entirely. Again, I can play 02 and all the other missing ones in Zune Marketplace, but they are still not recognized and collected.
So, any thoughts on what's happening with my MP3s?
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If you do want to try fiddling with them, I'd recommend MediaMonkey as a way of mass-editing and re-organising files; it's what I use whenever I get a new album I want to import into Zune.
What exactly do you mean by the missing items playing in Zune Marketplace? Is this from inside the library, or on the Marketplace entry for the album (i.e. there're boxes that say "In Collection" or "Buy"/"Download" next to each track)?
EDIT: For clarification - MediaMonkey can help with editing the tags on your files and sorting them into folders based on that, but it can't sync to the Zune device itself.
It's also possible that the tags are messed up in a way so as to confuse the library components of Zune. This can result in the track not showing up, although i've only run into this in a very specific case with a massive collection, myself. (it's related to how "various artists" get applied to compilation albums)
I'd mirror Ayulin's suggestion. You might get some benefit from retagging the offending files, and seeing if that helps.
As for the audiobooks, i'm not sure. I've only ever used audiobooks downloaded by Audible's software, and they end up under a specific audiobook category that does better tracking for the audiobook. I doubt that can be used to inject your own audiobooks however.
One big problem that the Zune software sometimes struggles with is when the "Album Artist" field is missing, or not consistent. For example, try opening up all of your Patrick Rothfuss mp3s, highlight them all, and check to see if Album Artist is filled in. It should be the same across the entire "album". And make sure the track numbers are correct as well. This is a little bit more of a manual process than using a program like MediaMonkey. MediaMonkey can be used to search through all of your mp3s to pick out inconsistencies, such as fields missing an artist. Personally, I've used both tools to get my mp3s nice and clean.
Good luck trying to get everything sorted out! I have a Zune and the Zune software as well, and orignally trying to get everything perfect took a while, but now all of my music is tagged perfectly. Even after an OS reformat, remaking my music library from all the mp3s went smoothly.