Operating System - WIndows 7 (whatever latest Service pack)
Version of CIS: the latest version of the 5.0 edition
Real time scanner: I use MBAM

and CIS
CIS settings - Same as the CLT guide in addition to having put the image execution control to untrusted / restricted
CLT score - 270
Note: I got bad results earlier aswell but this is a fresh install of 5.0 (prior to the 4.0 I had)
Results:
Date 01:36:04 - 01.01.2011
OS Windows Vista SP0 build 7600
1. RootkitInstallation: MissingDriverLoad Protected
2. RootkitInstallation: LoadAndCallImage Protected
3. RootkitInstallation: DriverSupersede Protected
4. RootkitInstallation: ChangeDrvPath Vulnerable
5. Invasion: Runner Protected
6. Invasion: RawDisk Vulnerable
7. Invasion: PhysicalMemory Protected
8. Invasion: FileDrop Vulnerable
9. Invasion: DebugControl Protected
10. Injection: SetWinEventHook Vulnerable
11. Injection: SetWindowsHookEx Vulnerable
12. Injection: SetThreadContext Protected
13. Injection: Services Vulnerable
14. Injection: ProcessInject Protected
15. Injection: KnownDlls Vulnerable
16. Injection: DupHandles Protected
17. Injection: CreateRemoteThread Protected
18. Injection: APC dll injection Protected
19. Injection: AdvancedProcessTermination Protected
20. InfoSend: ICMP Test Protected
21. InfoSend: DNS Test Vulnerable
22. Impersonation: OLE automation Protected
23. Impersonation: ExplorerAsParent Vulnerable
24. Impersonation: DDE Vulnerable
25. Impersonation: Coat Vulnerable
26. Impersonation: BITS Protected
27. Hijacking: WinlogonNotify Protected
28. Hijacking: Userinit Vulnerable
29. Hijacking: UIHost Protected
30. Hijacking: SupersedeServiceDll Vulnerable
31. Hijacking: StartupPrograms Vulnerable
32. Hijacking: ChangeDebuggerPath Protected
33. Hijacking: AppinitDlls Vulnerable
34. Hijacking: ActiveDesktop Protected
Score 190/340
BTW: I DO HAVE WINDOWS 7 NOT VISTA...