I know this is old and MichelleK10 may have already resolved this issue, but...
It looks like MichelleK10 was using the following document:
While scanning, messages appear in scan window: "Not fully scanned"/"Did not have permission to open the file"
http://www.symantec.com/docs/TECH91510
The permission-related messages are related to "hidden or protected files owned by Root, with or without restricted privileges" and wouldn't have to do with a scan failing to complete. The "defaults write /Library/Preferences/com.Symantec.NAVX IgnorePermPref -bool YES" command in the Symantec KB article merely stops those (harmless) permissions errors from displaying.
If you're getting "Could not write domain com.Symantec.NAVX" I would suggest trying to repair the permissions via Utilities > Disk Utility. This sounds more like an OS X problem than a SEP for Mac problem, or you may not be an admin user--may want to check Apple Support.
sandra