The 5th generation (Video) iPod has two partitions: a proprietary firmware partition followed by a FAT32 data partition. In the MBR of iPods formatted for Windows, the firmware partition has type 0. GParted considers it to be unallocated space. Because of that, it can easily overwrite the firmware partition or its partition table entry. That would be bad, because the firmware partition is needed, even when booting Rockbox or iPodLinux.
I first used fdisk to change the firmware partition type to a non-zero value. Then I could safely work with GParted without any danger of overwriting the firmware partition. Finally, when I was done, I set the type back to zero. Fdisk warns that you probably shouldn't set the type to zero, but it's really supposed to be zero.