If you use konqueror to copy files from ipod:/ to somewhere on the system, it will escape certain characters by converting them to %HH sequences.  (e.g / -> %2f)

If you have amarok scan the files, they will show up in the collection, but if you try to actually play or manipulate them, amarok will complain that it can't find the files locally.

The problem is that it's converted the %2f sequences back to / characters and tries to access the files with the wrong path.