Perhaps this, from MacFixIt, will help...
What are the steps that one should take before performing a system upgrade?
Answer:
1. Before running the update, check your startup drive for damage and repair it, if necessary. The easiest way to do this is to boot from the OS X Install CD and run Disk Utility (from the Installer menu). Click the First Aid tab, select your startup volume, and click "Repair Disk." (If you know how, you can instead start your Mac in single-user mode and use fsck, as this runs the same repair routines.) If you have a third-party disk utility such as Alsoft's DiskWarrior, you can also run that for good measure.
2. Before running the update, repair permissions on your boot volume. To do this, launch Disk Utility while booted from your normal startup drive, click the First Aid tab, and then click "Repair Disk Permissions."
3. Install the update.
4. After running the update, again repair permissions.
5. If you still have problems, try applying the combo updater for the current release (when it becomes available).
Harv