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It is absolutely essential to repair permissions before and after you run any update that uses Apple's installer application!
About Disk Utility's Repair Disk Permissions feature (Mac OS X 10.2, 10.3). Failing to repair permissions before you apply the 10.3.4, 10.3.5 or 10.3.6 updates can result in the situation that applications do not launch or unexpectedly quit. Once you face this situation a reinstall of the system might be necessary. Repairing permissions after these specific problems occur usually does not help.
Permissions can get broken by installations of third-party applications that use Apple's installer app.
If people use their OS 9 Classic folder to boot into OS 9 natively (e.g. to install required firmware upgrades) they also have a high probability of permissions being changed.
Furthermore there are many users who did simple upgrades since 10.0.x. 10.0 and 10.1 are known to do weird things to permissions.
So you might not need to repair permissions if you:
1. Never installed an application that asked for your password
2. Never did a simple upgrade
3. Never booted into OS 9 natively from the same systemfolder that you use as Classic.
In all other cases I do suggest you repair!
Reference (MacFixIt subscribers only): MacFixIt: Special Report: Troubleshooting Mac OS X 10.3.4
Some background information: Michael Conniff: Spurious Permissions errors in OS X 10.3
Permission Repair: The Full Story
Apple Mac OS X 10.3 Help: My computer keeps freezing or I see a flashing question mark: "It's a good idea to repair disk permissions as a regular maintenance task after upgrading or installing new software."
There are hints suggesting that corrupted cache files can also contribute to problems after system updates. Therefore you should consider to clean the cache files before you apply any system update with a utility such as Panther Cache Cleaner, Cocktail or OnyX.
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