Nessus reports a vulnerability because of 64-bit cipher suites and SSL Medium Strength Cipher Suites Supported (even though it shows up as strong). Windows requires the cipher TLS_RSA_WITH_3DES_EDE_CBC_SHA being disabled.

I found that adding the cipher suite to the registry didn’t work as expected. Then I found a reference that says it’s a different key based on the version of Windows. So I added both to our registry file to handle disabling it regardless.

Registry file:

Windows Registry Editor Version 5.00
[HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Control\SecurityProviders\SCHANNEL\Ciphers\DES 56/56]
"Enabled"=dword:00000000
[HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Control\SecurityProviders\SCHANNEL\Ciphers\RC2 40/128]
"Enabled"=dword:00000000
[HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Control\SecurityProviders\SCHANNEL\Ciphers\RC4 40/128]
"Enabled"=dword:00000000
[HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Control\SecurityProviders\SCHANNEL\Ciphers\RC4 56/128]
"Enabled"=dword:00000000
[HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Control\SecurityProviders\SCHANNEL\Ciphers\RC4 128/128]
"Enabled"=dword:00000000
[HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Control\SecurityProviders\SCHANNEL\Ciphers\Triple DES 168/168]
"Enabled"=dword:00000000
[HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Control\SecurityProviders\SCHANNEL\Ciphers\Triple DES 168]
"Enabled"=dword:00000000

Before:

$ nmap --script +ssl-enum-ciphers -p 3389 iprintsrvr -Pn

Starting Nmap 6.47 ( http://nmap.org ) at 2017-01-20 12:28 GMT
Nmap scan report for iprintsrvr (192.168.0.181)
Host is up (0.00051s latency).
rDNS record for 192.168.0.181: iprintsrvr.domain.local
PORT STATE SERVICE
3389/tcp open ms-wbt-server
| ssl-enum-ciphers: 
| TLSv1.0: 
| ciphers: 
| TLS_ECDHE_RSA_WITH_AES_128_CBC_SHA - strong
| TLS_ECDHE_RSA_WITH_AES_256_CBC_SHA - strong
| TLS_RSA_WITH_3DES_EDE_CBC_SHA - strong
| TLS_RSA_WITH_AES_128_CBC_SHA - strong
| TLS_RSA_WITH_AES_256_CBC_SHA - strong
| compressors: 
| NULL
|_ least strength: strong

Nmap done: 1 IP address (1 host up) scanned in 6.30 seconds

After:

$ nmap --script +ssl-enum-ciphers -p 3389 iprintsrvr -Pn

Starting Nmap 6.47 ( http://nmap.org ) at 2017-01-20 12:29 GMT
Nmap scan report for iprintsrvr (192.168.0.181)
Host is up (0.00028s latency).
rDNS record for 192.168.0.181: iprintsrvr.domain.local
PORT STATE SERVICE
3389/tcp open ms-wbt-server
| ssl-enum-ciphers: 
| TLSv1.0: 
| ciphers: 
| TLS_ECDHE_RSA_WITH_AES_128_CBC_SHA - strong
| TLS_ECDHE_RSA_WITH_AES_256_CBC_SHA - strong
| TLS_RSA_WITH_AES_128_CBC_SHA - strong
| TLS_RSA_WITH_AES_256_CBC_SHA - strong
| compressors: 
| NULL
|_ least strength: strong

Nmap done: 1 IP address (1 host up) scanned in 0.15 seconds

References

See Note For the versions of Windows that releases before Windows Vista, the key should be Triple DES 168/168.

https://support.microsoft.com/en-us/help/245030/how-to-restrict-the-use-of-certain-cryptographic-algorithms-and-protocols-in-schannel.dll