Yeah it seems that way.
The CD emulated portion of the device probably showed up as /dev/cdrom1 or /dev/scd1 or something and that's why it didn't show up in the list.
Sorry you went through all the effort with the linux boot disk and all. I've run into hard drives that had "special" partitions that couldn't be deleted in Windows, but they were just partitions marked as "read only". Blasting zeroes at the partition table using Linux worked great for that, but this is something different.