Hey I'd like to throw some boilerplate fixit text in here. And y'all can take it or leave it.
Essentially, jw, you've got to start over. Running that SecUpdate messed it up for ya.
And you've got to get your Mail v**4.5** back & back into the Applications folder & delete all other instances of Mail.app (duplicates, old versions from previous OSX's, etc.) and, for the sake of eliminating confusion after everything's fixed, all copies of Mail.app aliases wherever they are on your HDD.
THEN you can re-run the SecUpdate file & get your Mail up to snuff, to v4.6.
So here's the text. All of this is long, & boring & overdone to some I'm sure, but it covers all the bases.
2 parts: A & B. A is the Mail.app v4.5 recovery part, and B is the fix all the rest part.
The last extra part, Part C, will repair any Mail plugins, if you have any, that don't work for you after updating Mail to v4.6 & your Mail's back up & running again.
PART A: How to reinstall Apple Mail:
1. Do a HDD-wide search for all instances of Mail.app. Delete them all. However, should you happen to find a Mail.app v4.5 somewhere, move that to the Applications folder & wipe out all the rest of the Mail.app's, if any.
Wipe out all instances of aliases to Mail.app, too.
2. Get your OS-X Installation disk into your DVD drive.
Dbl-click "Optional Installs" in the window that comes up, & then dbl-click on the "Optional Installs" package file within that folder.
3. Click on "Continue" in the first two steps of the installation wizard.
Click "Continue" and then "Agree" to accept the license agreement.
In the "Select a destination" window click on your Mac's hard drive & then click on "Continue."
4. Click on the triangle icon next to "Applications" on the "Custom Install" screen to open up the list of Applications available.
Select the check box next to "Mail" and then click on "Continue."
Click "Install" to reinstall Apple Mail.
5. Restart your Mac.
6. Back at the Desktop, first run Disk Utility, select your harddrive, & click on Repair Disk Permissions.
When finished, run "Software Update..." under the Apple menu & install anything having to do with system file updates to ensure that your Mail.app is up to date (i.e., skip an iTunes or Safari update if you want to, for example).
PART B: Update OS-X & Mail v4.5 in particular to version 4.6 using the downloaded "Security Update 2012-004" file:
I went thru all this Security Update / post-update / DOA Apple Mail stuff late September, & I found the answer(s) thanks in part to others on here & I eventually got my Mail working just fine again, & fairly quickly, if you count the time it took to download the actual Security Update file as a time-consuming absolutely necessary step independent of however much time *that* frankly unforseeable & unexpected major necessary step took.
First, I'm going to assume that you've got Snow Leopard running on your Mac, since that OS is the only one with a recent Security Update (that I know of), & which has some people like yourself screamin' about their Mail not working anymore.
Essentially, the problem that you & I & others experienced with Mail after running the late September "Security Update 2012 004" for Snow Leopard is that the actual Mail.app, which without the Update installed is version 4.5, was *NOT* inside the root of the Applications folder. That's it...... believe it or not. All this trouble because of that. And since the Apple Security Update software writers' code looked for Mail.app v4.5 to be there and ONLY there, then when it didn't find it there, it just dropped into the App folder a half-baked, nonfunctional v4.6 Mail.app do-do.
So.... what you've got to do, in these chronological steps, is:
1. Find your Mail.app version 4.5 and get it into the root of the Applications folder (where Apple puts most of their apps).
NOTE: If you find an earlier version of Mail after doing the Mail reinstall from the Installation DVD (you probably will), you can run the 10.6.8 Combo Update v1.1 to update that older Mail to the one you previous had, to v4.5. I haven't clearly defined whether that step is absolutely necessary or not, or if running the "Security Update 2012-004" will update a version older than 4.5 up to 4.6. Best bet at this point though, really, is to go ahead & run the 10.6.8 Combo Update now, which will release you from having to run that Combo Update in the possibly necessary remedial steps after Step 4 below.
2. Find any and all other Mail.apps you may have on your Mac's harddrive, all versions (again, you may have a bogus, half-baked Mail.app v4.6 in your App folder after running the Update. Dump it.), and delete every single one of those other Mail.apps, should you find any more (i.e., duplicates, older versions than 4.5, etc).
All you must have is *one* Mail.app *only* existing on that harddrive, version 4.5, and it's got to be located inside the Applications folder. Dump *all* others throughout your Mac's harddrive. That includes, to avoid confusion down the road when Mail gets updated to v4.6, *ALL* aliases, too.
3. Download the "Security Update 2012-004" file from here:
http://support.apple.com/kb/DL1586
4. Install the Security Update & then do the mandatory reboot.
5. After rebooting & returning to the Desktop, your Mail.app inside the Applications folder should be updated to version 4.6 & it should work just fine. THEN you can remake your Mail aliases from that Mail.app & stick them wherever you want; just keep the Mail.app itself inside the App folder.
However, if you're one of the unlucky ones & those 5 steps don't work for you, then you're going to have to basically start over & add another few steps. You'll have to "refresh" your 10.6.8's system files first.
So start that process by doing Steps 1 & 2 all over again, and then reboot.
Back at the Desktop, download the "Mac OS X 10.6.8 Update Combo v1.1" from here:
http://support.apple.com/kb/DL1399
Install that Combo Update, which will rid your Snow Leopard of software glitches, including possibly your existing Mail.app version 4.5 which perhaps during the file-churning may have become un-upgradeable, and otherwise ensure 10.6.8's systemic integrity, and then do the mandatory reboot again.
After rebooting & returning to the Desktop, continue on with doing Steps 4 & 5 all over again, also.
Reboot, get back to the Desktop, & try out Mail by double-clicking it in the Apps folder. If it didn't work before, it certainly should work now. And if so, then *now* you can make your Mail v4.6 aliases & spread 'em around.
PART C: How to fix Mail plugins that don't work after the update of Mail to v4.6:
I've got several Mail plugins that did not work after running the "SecUpd2012-004" Security Update, which updated Mail.app from v4.5 to v4.6, and I'm sure there are others of you out there who ran into the same consequential problem.
Here is the downloadable fix I found, developed by Code2K:Labs:
From the Code2K:Labs site: http://code2k.net/products/mailpluginfix/
From MacUpdate: http://www.macupdate.com/app/mac/37804/mailpluginfix
Also, if you have plans to upgrade your Snow Leopard to Lion/Mountain Lion, Apple's got a new Supplemental Update for 10.6.8 out now that essentially will ready your 10.6.8 for the migration of your personalized stuff in Snow Leopard during the overwriting OS upgrading that occurs when you run the Lion/ML installer:
http://support.apple.com/kb/DL1429
I hope this helps, jw, & that my "intervening" in here with my 2 cents of help doesn't ruffle any feathers....
Happy Mac'in!
Kevin Kendall