So after some more fiddling with the ipod (it seems that it was being mounted in UTF8 and case sensitive mode?), I tried to use gnupod to init the database. No luck. When I try to remove the gnupod directory on the ipod, I get the following dmesg errors:
[105799.805514] sd 1:0:0:0: [sda] Result: hostbyte=DID_OK driverbyte=DRIVER_SENSE,SUGGEST_OK [105799.805523] sd 1:0:0:0: [sda] Sense Key : Medium Error [current] [105799.805528] sd 1:0:0:0: [sda] Add. Sense: No additional sense information It eventually manages to delete the directory, but after a long time (minutes) and with several "click-resets" along the way (ie nont normal behavior).