Mail won't close after security update

I just installed the recent security update (running 10.4.8) and now Mail won't close on either my Dual g% tower or on my iBook. In fact, both computers were unable to reboot after the install because the mail program needed to be force quit.
This was never a problem prior to the install of the security update.
Anyone have any ideas?
Thanks!

Problems arising right after installing a system update are usually the result of the problem already being there, or not having installed the update properly, or ignoring Apple’s "Important: Please read before installing" warnings, etc., rather than being caused by the update itself. In order to ensure that the update is installed properly, proceed as follows.
Verify/repair the startup disk (not just permissions), as described here:
The Repair functions of Disk Utility: what's it all about?
After having fixed all filesystem issues, if any, reinstall the update that appears to not have been installed properly.
Take a look at the following articles for guidelines on how to properly install system updates:
Troubleshooting installation and software updates
Installing software updates
Basically, you should verify/repair the startup disk before installing the update, no applications should be running while installing it, and you may experience unexpected results if you have third-party system software modifications (not normal applications) installed.
The above won’t solve the problem, but will allow us to at least troubleshoot it properly. Post back with your observations when done.
How many accounts do you have and what type are they (POP, IMAP, .Mac)?
In Mail, open Window > Activity Viewer. What do you see there when Mail refuses to quit? Actually, you may be able to avoid having to force quit Mail by canceling whatever it’s doing (by clicking on the red stop icon of the activity).
Do you have any Mail plug-ins or any system utilities that could interfere with Mail? In the Finder, go to each of the following folders (if they exist). What do you see there?
/Library/InputManagers/
~/Library/InputManagers/
/Library/Mail/Bundles/
~/Library/Mail/Bundles/
Note: For those not familiarized with the ~/ notation, it refers to the user’s home folder. You can easily locate any of the folders referred to in this post by copying the file path here, doing Go > Go to Folder in the Finder, and pasting the file path there.

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Mail won't open after Security Update 2012-004

At some point, Apple started doing this annoying stupid thing with certain app updates (among them QuickTime Player, and iTunes, and Mail) where if those apps do not reside in /Applications they will not be updated properly. In some cases, a new copy is installed in /Applications, and you just have to manually replace your older copy. Annoying, but doesn't break anything. I installed the latest security update today, after which Mail would not launch, with the error message, "You cannon run this version of Mail on this version of MacOS X." There was a new Mail item in /Applicaitons (my unupdated copy lives in /Applications/Communication) with a generic app icon that doesn't launch at all.
I tried copying the package contents from the new version to the old, but that didn't work. (Maybe if I'd logged out or restarted it would have, but I didn't try that.) I called Apple and they had me download a combo update. That did absolutely nothing except waste my time. I called back, and a Mail Specialist said I would need to archive and install from the original disc that came with my computer.
Bad support is so much worse than no help at all. If you don't know what you're doing are not skilled and just reading from a horrible, unhelpful script, say so, and don't make bad suggestions. What a waste of time A. to call support, B. to follow their suggestions, C. it would have been to follow the last of their suggestions.
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Run the installer
That's it. That's what support should have told me to do. Of course, shouldn't have had to do this at all; Software Update should be smart enough to update apps wherever they live.

At some point, Apple started doing this annoying stupid thing with certain app updates (among them QuickTime Player, and iTunes, and Mail) where if those apps do not reside in /Applications they will not be updated properly.
Correct. It has always been that way in OS X. Applications, particularly from Apple, belong in the Applications Folder, where update installers can find them and link to associated system files that may be updated as well without you realising it.

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Installing a system update while you continue using the computer as if nothing was going on there is a really bad idea.
Verify/repair the startup disk (not just permissions), as described here:
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Hi Barry,
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Welcome to the Apple Support Communities
http://support.apple.com/kb/TS4424

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If the drive is OK then quit DU and return to the installer. Proceed with reinstalling OS X. Note that the Snow Leopard installer will not erase your drive or disturb your files. After installing a fresh copy of OS X the installer will move your Home folder, third-party applications, support items, and network preferences into the newly installed system.
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The first thing to do would be to boot from the Install & Restore disc that came with your machine by:
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2. After the machine has booted, pick your language, and when the Installer window appears, do not press Continue, but go to the Utilities menu in the menubar and open Disk Utility.
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I had to run to dinner... left you kind of hanging ;-(
I was afraid that you were still using your drive (and downloading files etc) while it was in a "precarious" state (thin ice, and jumping up and down to see how thin or thick the ice is... ).
Should always work from another disk drive.
Even if Disk Warrior repairs you want to try to backup files you need first. And it can help to trash stuff that you don't need, easy to replace. Sort of "peel an onion" tearing away the latest additions and working backward (in time to older files) to "undo" changes to the drive and directory.
There are some programs that will force a system to always boot into single user mode or verbose mode. I think Onyx and Cocktail, probably Tiger Cache Cleaner as well.
My feeling is that if there are problems, I avoid the Archive & Install entirely. I much prefer the ERASE with ZERO-ALL and restore from backups. Lacking that, full clean install. Backup along that way.
Backup or clone when you have the system installed.
When it has been updated to latest Apple version and patches.
Again when you have your essential programs installed.
And repair permissions as you go.
A system only takes up 15-45GB so you can even backup to a disk image (sparseimage is best).
You should be working from another drive now. FireWire or internal SATA.
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Backup (SuperDuper) to another drive first if possible.
Boot from that (free to do full copies) and make sure it works.
Always a "bad idea" to repair a drive w/o backups.
You always want to have current set of backup(s).
Run Disk Warrior from hard drive, not from CD.
Often, just the process of cloning a drive is enough.
Run Disk Warrior against the new clone backup.
Disk Warrior is good preventative maintenance and best choice when it gets beyond that to needing to repair a drive.
So first - have a couple backups. And second - buy SuperDuper ($29) so you can do faster smart updates regularly (rotate your backup set) - and finally Disk Warrior.
I've found Disk Warrior finds and fixes things that Disk Utility misses that can help. And SuperDuper is super easy and reliable.
And just because Disk Warrior (or any disk repair) "fixes" a drive doesn't mean you may not have the contents of files that are corrupt.
You don't use Disk Warrior after reformatting, you use it to rebuild the disk's directory (or catalogue).
DW can also check for drive's status and show how many spare blocks are left, in use, or attempts to reallocate. It does not show read errors or soft errors, but it shows overall SMART status.
Disk Warrior is a "one trick" (rebuilt directory) but it does an excellent job and checks some other area's of the filesystem.

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I presume when you were doing the Repair function booted from the CD that eventually you said "Repair" and it scanned the drive and said in green, "No problems found" or similar stuff.
Another way to effect repairs is to hold down the Shift key at Startup, which does a Disk Repair as it starts up, so it takes a while longer that usual, then loads the smallest-possible set of extensions and boots into "Safe Mode".
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Mail won't close after security update

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