There was a windows share (not ntfs) set up on C: which I took off. Then when I ran net share from the command prompt the C$ Default share was missing as well as the other share I had taken off.
However after playing around for a bit I found out how to restore the C$ share:
1. In Control Panel, double-click Administrative Tools, and then double-click Computer Management.
2. Expand Shared Folders, right-click Shares, and then click New File Share.
3. In the Folder to share box, type the path of the folder that you want to share, or click Browse to locate the folder.
4. Type the share name that you want to use followed by a dollar sign, and then click Next.
5. To make the share accessible to administrators only, select the Administrators have full control; other users have no access check box, and then click Finish.
6. Click Yes to create another share, or click No to return to the Computer Management console.