On the server, open an admin command prompt and run "net share" to see if those shares exist or not.
Check the registry key listed in this article to see if someone disabled the admin shares.
If the shares exist, then using an admin account on some other pc, use Powershell to test to see if you can access them.
Get-ChildItem -Path '\\servername\c$'
If that fails, test to see if the firewall is blocking access to port 445.
Test-NetConnection -ComputerName servername -CommonTCPPort SMB
If everything works ok, then it would appear that Nessus is not using an administrator account to authenticate to the server. Check the security eventlog on the server for logon failures when you run a scan. Refer to the Nessus documentation as to how to configure it for scanning.