Realtime protection and a scheduled scans are two very different things to Norton, CA, Panda, McAfee, AVG, and other AV programs.
A scheduled scan (or manual scan) will inspect everything unless you configure the scan to exclude directories (like a movie directory you know is clean that might take two hours to scan).
Realtime scanning is the scanning in realtime, of files and directories, in the background as they are opened and closed.
With all of these AV programs, scanning certain files and folders, will significantly slow down performance.
The Windows System 32 directory in XP and Vista is usually excluded from realtime scanning as per anti-virus program manufacturer recommendations. The programs to NOT default to this as it could open the manufacturer up to potential legal issues but in the advanced instructions there will be specific directories or files that are recommended to be excluded from realtime protection.
In Vista, some programs such as Adobe Writer and Quick Books will hang periodically if the hidden program files data directory is not excluded from real time scanning. Basically the symptom is the blue "rolling donut" just staying on the screen and not shutting down properly. Each program may or may not have specific exclusions that need to be entered into the anti-virus program exclusion list.
If you look at a default Norton installation often you will see that c:\windows\system32 is excluded by default (for example). This is because opening and closing files in that directory will slow down a system substancially. Incoming and outgoing files (to and from) that directory are scanned, but the act of opening an existing file is allowed without being scanned. This way the system works more quickly as the anti-virus program assumes a file being opened was already scanned when it was placed in the directory.
Sorry to be so long winded but I had a real tough time last year getting Quick Books 2008 to function on a Vista 64 computer and Intuit had no answers...
I arrived at my conclusion after examining several Microsoft Exchange email servers and discovering that certain files were excluded from scanning to improve performance and reduce data corruption. The concept of exclusions is a standard practice in the IT industry but each computer is slightly different in regards to programs, operating systems, updates and patches.
I hope this helps clarify my response.