I came across an issue recently when trying to run a Disk Defrag on my Windows 7 Machine.
As you can see below it did not show my OS Drive in Disk Defragmenter (In my case it should be C: )
The first thing i did was run a CHKDSK in read-only mode to see if there were any issues and the results showed that there was a corrupt record.
I then ran chkdsk /f so that it would fix these errors for me , please note this requires a reboot.
The CHKDSK fixed the error i was receiving, i then re-tried opening Disk Defragmenter and the OS drive was there