I have Safari 4.1.3 (4533.19.4). I checked my Preferences, and only the Appearances panel comes up -- no other options. What happened and how do I get all the preferences back?

Uninstall SIMBL as follows.

Select Go ▹ Go to Folder… from the Finder menu bar, then enter the following text in the box that opens:

/Library

A folder will open. From that folder, delete the items listed below (some may be absent.) You may be prompted for your administrator login password.

Log out and log back in.

Make sure you never reinstall SIMBL. It’s likely to come bundled with another third-party system modfication that depends on it. If you want trouble-free computing, avoid software that makes miraculous changes to other software, especially built-in applications. The only real exception to that rule is Safari extensions, which are mostly safe, and are easy to get rid of when they don’t work. SIMBL and its dependents are not Safari extensions.

I can only offer limited help because your OS X version is so old.

Please read this whole message before doing anything.

This procedure is a test, not a solution. Don’t be disappointed when you find that nothing has changed after you complete it.

Step 1

The purpose of this step is to determine whether the problem is localized to your user account.

Create a new, temporary user account and log into it. While logged in as the new user, you won’t have access to any of your personal files or settings. Applications will behave as if you were running them for the first time. Don’t be alarmed by this; it’s normal.

Test. Same problem(s)?

After testing, log out of the test account and, in your own account, delete it and its home folder.

Step 2

The purpose of this step is to determine whether the problem is caused by third-party system modifications that load automatically at startup or login.

Disconnect all wired peripherals except those needed for the test, and remove all aftermarket expansion cards. Boot in safe mode* and log in to the account with the problem. The instructions provided by Apple are as follows:

1. Be sure your Mac is shut down.
2. Press the power button.
3. Immediately after you hear the startup tone, hold the Shift key. The Shift key should be held as soon as possible after the startup tone, but not before the tone.
4. Release the Shift key when you see the gray Apple icon and the progress indicator (looks like a spinning gear).

Safe mode is much slower to boot and run than normal, and some things won’t work at all, including wireless networking on certain Macs.

The login screen appears even if you usually log in automatically. You must know your login password in order to log in. If you’ve forgotten the password, you will need to reset it before you begin.

Test while in safe mode. Same problem(s)?

After testing, reboot as usual (i.e., not in safe mode) and verify that you still have the problem. Post the results of steps 1 and 2.

Please read this whole message before doing anything. I'm not sure how much of this will work on your old system, but it won't do any damage.

This procedure is a diagnostic test. It won’t solve your problem. Don’t be disappointed when you find that nothing has changed after you complete it.

Third-party system modifications are a common cause of usability problems. By a “system modification,” I mean software that affects the operation of other software — potentially for the worse. The following procedure will help identify which such modifications you've installed. Don’t be alarmed by the complexity of these instructions — they’re easy to carry out and won’t change anything on your Mac.

These steps are to be taken while booted in “normal” mode, not in safe mode. If you’re now running in safe mode, reboot as usual before continuing.

Below are instructions to enter some UNIX shell commands. The commands are harmless, but they must be entered exactly as given in order to work. If you have doubts about the safety of the procedure suggested here, search this site for other discussions in which it’s been followed without any report of ill effects.

Some of the commands will line-wrap or scroll in your browser, but each one is really just a single line, all of which must be selected. You can accomplish this easily by triple-clicking anywhere in the line. The whole line will highlight, and you can then either copy or drag it. The headings “Step 1” and so on are not part of the commands.

Note: If you have more than one user account, Step 2 must be taken as an administrator. Ordinarily that would be the user created automatically when you booted the system for the first time. The other steps should be taken as the user who has the problem, if different. Most personal Macs have only one user, and in that case this paragraph doesn’t apply.

Launch the Terminal application in any of the following ways:

☞ Enter the first few letters of its name into a Spotlight search. Select it in the results (it should be at the top.)

☞ In the Finder, select Go ▹ Utilities from the menu bar, or press the key combination shift-command-U. The application is in the folder that opens.

☞ If you’re running OS X 10.7 or later, open LaunchPad. Click Utilities, then Terminal in the page that opens.

When you launch Terminal, a text window will open with a line already in it, ending either in a dollar sign (“$”) or a percent sign (“%”). If you get the percent sign, enter “sh” and press return. You should then get a new line ending in a dollar sign.

Step 1

Copy or drag — do not type — the line below into the Terminal window, then press return:

kextstat -kl | awk '!/com\.apple/{printf "%s %s\n", $6, $7}'

Post the lines of output (if any) that appear below what you just entered (the text, please, not a screenshot.) You can omit the final line ending in “$”.

Step 2

Repeat with this line:

sudo launchctl list | sed 1d | awk '!/0x|com\.(apple|openssh|vix)|edu\.mit|org\.(amavis|apache|cups|isc|ntp|postfix|x)/{print $3}'

This time, you'll be prompted for your login password, which won't be displayed when you type it. You may get a one-time warning not to screw up. You don't need to post the warning.

Note: If you don’t have a login password, you’ll need to set one before taking this step. If that’s not possible, skip to the next step.

Step 3

launchctl list | sed 1d | awk '!/0x|com\.apple|edu\.mit|org\.(x|openbsd)/{print $3}'

Step 4

ls -1A /e*/mach* {,/}L*/{Ad,Compon,Ex,Fram,In,Keyb,La,Mail/**,P*P,Priv,Qu,Scripti,Servi,Spo,Sta}* L*/Fonts 2> /dev/null

Important: If you formerly synchronized with a MobileMe account, your me.com email address may appear in the output of the above command. If so, anonymize it before posting.

Step 5

osascript -e 'tell application "System Events" to get name of every login item' 2> /dev/null

Remember, steps 1-5 are all drag-and-drop or copy-and-paste, whichever you prefer — no typing, except your password. Also remember to post the output.

You can then quit Terminal.

I doubt that the plugins are causing your problem. Don't bother checking for updates. There haven't been any for 10.4 in years, and there will never be one again.