Kernel  OS Vector5.9  I compiled libgpod 0.6.0 and gtkpod 0.99.12 myself with no errors.
I used mount -t vfat shortname=mixed and got some files to transfer to the iPod but they appeared
as "orphaned" and there were errors due to failed write permissions with others.
When I check the iPod I don't see any of the gtkpod transfered files.
Could it be a new firmware from Apple?  This device was purchased a week ago and initialized with
WindowsXP iTunes (7.6 I think).  Is there a way to reinitialize it with gtkpod? Many commands in 
gtkpod give errors (despite the vfat fix and chmod a+w for /mnt/ipod ).
Did Apple modify the iPod firmware to break compatibility with libgpod/gtkpod?  
Should I try the development versions of these packages?
What does "mount | grep /mnt/ipod" output?  There is a shortname
option for vfat filesystems.  The default is lower, which seems to
work fine for me.  Poking my iTunesDB, I even see that the path for my
tracks uses an upper case F, while ls shows a lowercase f.

What OS/distro are you using?