When you choose the mount point for the iPod in the GUI file chooser, make sure that you double-click 'IPOD' - else the mount point might end up as '/media'.
AFTER YOU CLOSE Exaile, check this by looking at ~/.exaile/settings.ini - make sure you have a line like -
ipod_mount = /media/IPOD
(if you get it wrong, it might say 'ipod_mount = /media')
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