From Microsoft:A basic disk's status is Not Initialized.
Cause:The disk does not contain a valid signature. After you install a new disk, the operating system must write a disk signature, the end of sector marker (also called signature word), and a master boot record or GUID partition table before you can create partitions on the disk. When you first start Disk Management after installing a new disk, a wizard appears that provides a list of the new disks detected by the operating system. If you cancel the wizard before the disk signature is written, the disk status remains Not Initialized.
So I believe you are correct in that Windows has created a registry entry for that drive without the Disk Signature in one of the keys.
You could try and find that key in a registry search if you search for the name of the hard drive manufacturer or serial number (a long shot, and it would be best to be the only drive in your system of that brand). You would need to be very careful to be sure you are not deleting a key for one of the other drives.
Or you could just click to initialize the (missing) disk and Windows might ignore it afterward. The danger here is that you would want to be sure that only the phantom disk is initialized, not a real disk. So you should disconnect any addition drives and only have your C: partition drive connected if you decide to try this. I've never tried it, but I don't believe Windows will allow you to initialize the system drive while it is running (not promising anything).