I tried to add a folder of music to my ipod shuffle, and it didn't show up in amarok's view of the ipod and is not on the ipod itself. Now, every time I try to add that folder again, amarok says the files are already there, even though the ipod was emptied in amarok and shows up empy in amarok.

EDIT: actually, tracks I've never added to the ipod also result in amarok telling me they are already on the ipod as well

Could you please be more explicit about the Amarok and KDE version as well as the version of your iPod?

I have Amarok 2.4.3 and KDE 4.7.4. My ipod shuffle is 2nd generation. I don't know if it makes a difference, but I'm running Ubuntu 11.10 with the XFCE desktop.

Amarok 2.4.3 is really old, and iPod support was broken. Update to the current version and it should work fine. (The easiest way of doing this is to update Ubuntu to the current version and add ppa:kubuntu-ppa/backports.)

Do you mean upgrade Ubuntu to 12.04 (or whatever the current version is), or just update? Upgrading Ubuntu usually causes problems.

Upgrade to 12.04 (or shortly, 12.10). Recent versions of Amarok don't get packaged for old versions of Ubuntu.

I think I've found the problem. Most of my music files are in flac format.

Thanks for the help.