The only proper, and well documented, way to install a major update pack since day 1, is not to do it from software update. You should always install it after downloading the combo updater and follow the procedure below. This will greatly reduce, or eliminate, chances for problems:
Download the combo updater and follow the following method:
1. Run disk utility and do a verify disk, and if clean, a repair permissions.
2. reboot the machine
3. apply the combo update
4. after reboot, rerun disk utility and repeat verify disk and repair permissions.
5. reboot
6. run software update and apply any other patches.
If you decide to take the chance and run the software update package, do that at step 3 (instead of the combo update).