Curious. Do you have Zune syncing a music folder automatically? I selected individual albums to sync and don't use a media server but may experiment to see what happens if I move an album to another location.
I'm not sure what you mean. I don't know of a setting in Zune to tell it to sync or not to sync. I pointed it to the Music folder on my media server for music, photos and videos. It automatically looks there for my media and stores there when I buy or download something. This computer has Windows 7, which shows both local and media server files in the Windows 7 library. So when I look at my music library it shows both the C: drive and my media server.
There is another annoying thing that happens when my computer loses connection with the media server. If I buy or download something, rather than warning me that my default folder is not available, it just decides for itself where to store the files. So I have to go looking for the files in the Windows 7 library to move them to the media server later.
But when I do move them back to my media server, Zune automatically finds them and updates the collection. I just move the folders in Windows Explorer and Zune does the rest.
Windows 7 is actually really good about using the media server. In fact, if you use a common username and password between the two, it's seemless. This started happening when I installed Serviio Media Server add-in on my media server. I uninstalled it and hopefully that fixes the problem.