You might simply need to reset the metadata on the files.

In the 2.0 Emplode software, select the "All tracks" view, select all of the tracks, then right-click on them and hit "reset metadata".

You will have to do maybe one or two synchs after this to get it to rebuild the structures.

After you have done this, let us know if it worked. If so, I will make a FAQ entry on the subject.