Software Update may not always work properly. Either sometimes it seems to miss specific updates or it claims the updates are already installed. People who have been affected by this problem have tried numerous approaches to fixing it, including booting to Safe Mode, running permissions fixes, and even resetting hardware settings; however, nothing has helped them.
Most Software Update problems are not with permissions or with other programs or system features, so a permissions fix and using Safe Mode usually will not help the problem. Generally, Software Update problems happen when there is an error with the receipt files associated with previously installed updates, or if a receipt file is corrupt, it will prevent new updates from installing.
Most of the time, you can fix these problems by managing new or recently altered receipt files on the system, as well as other settings and temporary files used by Software Update.
Software Update recognizes installed updates regardless of whether a receipt file exists for it. These receipts are small package files that contain information on what items were installed, what their permissions are, and the size of the items. If an installation fails and the receipt is left behind, Software Update may not show the update as being available. Go to the /Macintosh HD/Library/Receipts/ folder and locate the .PKG or .BOM file that is associated with the update and remove it.
Keep in mind that other services may use receipts--such as Disk Utility's "Permissions Fix"--so do not remove the ones that are not associated with the problematic updates. If no updates work, you can try moving all the receipts from the receipts folder and test Software Update again, but keep them around and replace them if they are not contributing to the Software Update problem.
Remove downloaded updates
Update-related files may also be in the /Macintosh HD/Library/Updates/ folder, in a subdirectory with a title like "61-7680." In each folder you should have a .DIST file along with the install package for the update. Remove any update files from this folder that are associated with the missing updates, and try running Software Update again.
Remove preference files
A corrupt preference file can cause Software Update problems, so you can try removing this file to see if it helps. The preference file holds information about ignored updates, so if you are having problems with ignored updates not sticking, removing this file may help. The preference file is called "com.apple.SoftwareUpdate.plist" and is located in the /Macintosh HD/Library/Preferences/ folder. Remove the file from this folder and try Software Update again.