If you're using playlists that reference iTunes-transferred music then the strange filenames are expected. This is because Apple changes the names to obscure them. Rockbox shows what the file is by the name it has on the disk.
The best way around this is to use Rockbox when transferring music as you can then call each file by a sane name. Although this means that you (probably) won't be able to use these songs under the Apple firmware.