Menu Bar Items Missing after Safari 3.1 update

Question

Installed Safari 3.1 and restarted; menu bar items Time, Date, and Volume icon are now missing, and Safari 3.1 and Mail crash on launch. Trashed com.apple.systemuiserver.plist and restarted--no difference.
Tried reinstalling the 10.4.11 PPC update and Safari 3.0.4 and Mail now work, but menu bar icons still missing. System Preferences for these items stick, but nothing appears in menu bar. This seems to be a recurring issue with Mac OS X, but Apple isn't helping people by telling them how to fix it, or changing their updates so it doesn't happen to begin with.
Ideas or suggestions to fix this are appreciated.
Mulder

Answer 1

What are permissions?
Every file and folder on a Mac OS X hard drive has a set of permissions—settings that determine which user(s) have access to each item, and exactly what that access is. For example, permissions dictate whether or not a particular user can open and edit a particular file. But permissions also determine which items the operating system—or specific parts of it—can access and modify, and which files are accessible by applications.
What does repairing permissions do?
The Repair Disk Permissions function—the process that actually performs the task of repairing permissions—examines certain files and folders on your Mac’s hard drive to see if their current permissions settings are what Mac OS X expects them to be; if discrepancies are found, the offending permissions are changed to match the expected settings.
(In Mac OS X 10.3 and later, repairing permissions also performs one other, unrelated, task: If the invisible /tmp symbolic link—which is linked to the /private/tmp directory—is missing, the link will be recreated.)
Why is it necessary to repair permissions?
If permissions on particular files are “incorrect”—i.e., not what Mac OS X expects them to be or not what they need to be for your Mac’s normal operation—you can experience problems when the operating system tries to access or modify those files. For example, you may have trouble logging in to your account, printing, launching applications, or even starting up your Mac. Similarly, if an application—from Apple or a third-party developer—needs access to a particular file or folder to function, and the permissions on that item have changed in a way that prevents such access, the application may not function properly (or at all). The Repair Disk Permissions function can fix such problems by ensuring that certain files have the correct permissions.
There’s also a security element here: Many system-level files have permissions set a particular way so that applications or users that shouldn’t be meddling with those files can’t. If the permissions on certain system-level files somehow get changed so that access to those files is no longer restricted, you’ve got the potential for a major security issue. Repairing permissions can resolve such issues by resetting permissions on those files to prevent unauthorized access.
How do I repair permissions?
The Repair Disk Permissions function is part of Apple’s Disk Utility (in /Applications/Utilities). After launching Disk Utility, select the desired disk—generally your startup disk—in the list to the left, then click the First Aid tab. At the bottom of the First Aid panel, click the Repair Disk Permissions button. (You could instead use the Verify Disk Permissions option to preview any potential repairs before performing them, but for most users there’s little benefit from this extra step.)
Permissions can also be repaired via the shell (Terminal) by using the command sudo diskutil repairPermissions /. However, it’s unlikely that the typical user will ever need to perform the task in this manner. It’s useful if for some reason Disk Utility itself won’t launch, or for repairing permissions on a remote Mac when connected via Remote Login (SSH), but otherwise you’re just as well served using Disk Utility.
How does the Repair Disk Permissions function know what the “correct” permissions are?
When you use Apple’s Installer utility to install software (such as Mac OS X itself or an OS X update), the installation package (the .pkg file you double-click to begin installation, or that Software Update downloads in the background for an automatic installation) generally leaves behind a receipt—a smaller Mac OS X package that includes information about every file installed, including the permissions each file should have. This receipt is placed in /Library/Receipts. When you run the Repair Disk Permissions function, it examines the receipts in the /Library/Receipts directory of the disk being repaired—which means the feature works only on volumes with Mac OS X installed—and compares the information in the receipt with the actual files on your drive. If the Repair Disk Permissions function finds a file with permissions that differ from what a receipt claims they should be, that file’s permissions are reset to their receipt-specified values. (If you’re curious about the information contained in a receipt, the easiest way to view it is to use the utility Pacifist; simply drag and drop the appropriate receipt into the Pacifist window and you’ll be presented with a list of all files installed by the similarly-named installation package, along with each file’s original permissions.)
It’s worth noting here that although the function is called “Repair Disk Permissions,” what is actually happening is that files’ permissions are being reset or restored to a particular state. It’s possible—though not common—for a particular file’s permissions to differ from what a receipt claims they should be without those permissions actually being “broken.”
Are all files affected by Repair Disk Permissions?
No. As you may have inferred from the above description, only those files installed using OS X’s Installer utility and whose installation packages leave behind a proper receipt in /Library/Receipts are affected by the Repair Disk Permissions function. This means that most of the files affected by the Repair Disk Permissions function are system-level files, application files, or system add-ons—not applications installed by drag-and-drop, and not your documents or other user-level files.
If repairing permissions is useful in general, why doesn’t Apple recommend it as routine maintenance?
Apple does, quite explicitly:
It’s a good idea to repair disk permissions as a regular maintenance task after upgrading or installing new software.
That’s taken from Mac Help—in both Panther and Tiger—right on your Mac. Similar statements can be found in other Support articles, one of which is:
http://docs.info.apple.com/article.html?artnum=25751