Dunno if this will help but:
I don't recognize the dialogue box on your screenshot- & can't remember the exact dialogues I saw when I had the problems. But Debian & Ubuntu are similar.
See whether you can copy a file to your ipod from console, anything will do, doesn't have to be a .mpg as you're just testing. If you can't, try umounting & remounting to a directory you've created for that purpose, then try again. If it works, you can try deleting it, to establish whether you, or gtkpod, or any application, will be able to affect anything on your ipod. I think this is worth a go before you try to rewrite the ipod filesystem.
And welcome to LQ!