I recently install FC6, and have been using amarok to manage the shuffle without any problems.

However, since doing an update (Nov 21) I can no longer use amarok with my shuffle.

It'll read the shuffle db fine, but doesn't remove the songs or update the db when I remove songs.  If I repair, it does find the orphaned songs and remove them when I delete them.

Starting with a clean shuffle (via restore, done from a Windows box), I tried to add songs, transfer to the shuffle, then unmount it - the result is th shuffle doesn't play anything.  It looks like the db isn't getting created properly.

For what it's worth, the update installed libgpod.i386 0.4.0-0.fc6.

It's not the hardware, because I have no problem adding songs using gtkpod or banshee.

Any ideas?

It's very probably that the update upgraded libgpod, but not Amarok - which probably was compiled against libgpod 0.3.2. The symptoms you describe are typical of this situation.