yes I run fsck.vfat on filesystem and made sure it's clean.
I can add, that some programs (like parted) do not support logical sector size (LSS) of 2048, and only support LSS of 512.
My Ipod's fat32 partition is formatted with LSS of 2048, because mkfs.vfat sad that this hardware does not support other LSS.
I do not know exactly that problem is in logical sector size. Because other users with Ipod video 30GB have everything alright with rockbox, no? It's interesting if their partition size was detected right and what logical sector size their partition have.