After Crash: Mail opens to setup assistant, Where is everything?

Question

I shutdown and rebooted my computer after it did not want to take my password; the keyboard wasn't responding. Mail was open at the time I did this and after rebooting, when I open Mail it give me the setup assistant! In Library/Mail everything that should be there is there, my folders, my accounts... why is Mail not seeing this info and not opening it correctly? What happened? I can't see anything in the log and repairing disk permissions didn't work.
I have a back-up but it's at least a month old, maybe more. Seeing as my files are in the Library, I don't understand why Mail isn't working correctly.
Any help is appreciated as I am seriously freaking out.
Thank you!

Answer 1

What happened is that, probably as a result of what you did, Mail discarded the ~/Library/Preferences/com.apple.mail.plist preferences file and created a new one. This file is where all the account settings (but not the messages themselves) are stored. As a result, all your non-.Mac account settings are lost.
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, and making sure that there’s enough space available on the startup disk (a few GB, plus the space needed to make a backup copy of the Mail folder), quit Mail if it’s running, and make a backup copy of the ~/Library/Mail folder, e.g. by dragging it to the Desktop while holding the Option (Alt) key down, just in case something else goes wrong while trying to solve the problem. This is where all your mail is stored.
You have three options now:
(1) Restore com.apple.mail.plist from a backup if you have one. Mail shouldn’t be running while you do this.
(2) Set up your non-.Mac accounts in Mail again. If given the option to import existing mailboxes or something like that, don’t. Just enter the account information and Mail will automagically rediscover the data in ~/Library/Mail/ when done. You’ll also have to re-configure most of your settings in Mail > Preferences. For spam-related security reasons, the first thing you should do is go to Preferences > Viewing and disable Display remote images in HTML messages if it’s enabled.
(3) Mail may have renamed the old preferences file to com.apple.mail.plist.saved. If that’s the case, you may try moving the new com.apple.mail.plist out of ~/Library/Preferences/ (e.g. to the Desktop) and rename the old com.apple.mail.plist.saved back to com.apple.mail.plist. Again, be sure Mail isn’t running while doing this. Since Mail decided to discard it, I would expect this file to be corrupt (I don’t understand why would Mail discard it and create a new one otherwise), but apparently that often is not the case and the settings can indeed be restored by just renaming the file.
Note: For those not familiarized with the ~/ notation, it refers to the user’s home folder, i.e. ~/Library is the Library folder within the user’s home folder.