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I recently sent my Apple MacBook Pro (Retina 15" mid-2012 with OS X 10.8.3) in to Apple to repair the screen, and they wiped the hard drive. I connected my external Time Machine drive and booted into recovery mode to restore the backup taken right before I handed the machine in.

However, there are numerous instabilities/errors in the restored system: 'usernoted' crashes, re-launches, and crashes again, endlessly; Dropbox forgot my login information; Apple Mail acts like it is being run for the first time; and so on.

What can be going wrong here? The only error in the Install Log during restore is "NSSoftLinking - The Librarian framework's library couldn't be loaded from (null)". I've tried restoring three separate snapshots and resetting the PRAM, but saw no difference difference. I have never manually excluded any folders from my Time Machine backups.

The external Time Machine drive did take a fall when it was powered off, but Disk Utility reports no errors on the disk, and repairing it doesn't fix anything.

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Additionally: I notice that during the restore process, the progress bar get to around 68%-70%, then immediately jumps to the "Restore completed, please reboot" dialog. Don't know if that's normal. –  int3h Mar 30 '13 at 2:46
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I (partially) figured out what was up. It looks like Time Machine doesn't properly detect when symlink sources change.

I use a script called homesick to keep my configuration files under version control. homesick keeps the actual files in a git repository, and symlinks the original files to the repository's version.

At some point in the past, I changed which repo I was using, which caused the location the symlinks were pointing to to change, but otherwise left them unchanged.

Time Machine backed up the symlinks when they were first created, pointing to the first repo. However, when homesick changed the source of the symlinks, Time Machine did not register the change, and didn't backup the new versions.

Thus, all my configuration files were symlinks pointing to now nonexistent files. This caused most of the weirdness I was seeing in my restored system.

I still don't know why Dropbox and Mail.app acted as if they were being run for the first time. However, after clicking through their configuration wizards, my data in both was as I left it.

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