GTK Pod not reading my control/media/ipod file

I just got this GTK Pod program. I then put a few songs on my ipod. I realized that when i was done, the songs were not in order. So i go back into the program and adjust the files (that are already on the ipod from my last sychronization/save data) and now it tells me it cant open the control/media file where all my songs are stored. How is this fixed? I tried uninstalling the program and reinstalling it.