All system preferences / settings lost after restore

Maybe I'm missing the point, but I had to run a restore last night after a hanging software update. Basically what happened was I was running normal software update (tryna get that iPhone os update), and it got hung up installing something. I was forced to restart, and the machine would not restart...
So after going thru the requisite repair disk permissions and AppleJack to find my startup disk was not corrupted and still in fact had data on it (yet still couldn't restart) I just reverted my system to a pre-backup version via Time Machine, a backup that had occured just hours prior.
While I did not lose any data, I did lose:
- my default itunes library was reset (i keep my music on a separate internal disk, I had to manually add all my music into the library)
- extensions / bookmarks / settings / saved passwords in Firefox, Coda, FTP programs, etc
- haven't checked yet, but possibly Apache / Ruby installs on my startup disk too
- Dock / desktop background / mouse configuration / network configuation etc.
It's basically like a new computer but with my old files and applications installed on it.
is just how time machine works? i'm glad i didn't lose any data, but it's a real pain to set everything up the way i had it before...
any insight would be rad!

Colin Bayer wrote:
* I got home at ~8:30 PM to a screen that still said "Copying ..." some 100,000 files and no progress all day. Finder was frozen, couldn't do anything. had to hard restart
That sounds like corruption on your backups, but given what happened next, I don't think so:
* now i'm getting the "no" symbol upon startup. great, that means it can't find os X on my startup disk. it goes to the next available startup disk, which happens to be another internal drive with windows XP on it.
That wouldn't be caused by the problem restoring Application Support.
* i boot from the install disk again. run disk repair. install disk doesn't even show a formatted / S.M.A.R.T. verified disk in HD Bay 1. somehow hard restarting just totally ruined my startup disk...damnit.
* i can't even start in single user mode.
* try to erase and/or re-partition the startup disk from the Disk Utility on the CD, and can't do that either. it gives me some resource busy error. this appears to be a Leopard bug and fortunately I can reformat from the snow leopard install disk.
I'm very suspicious of your internal HD. Try this: Intel-based Macs: Using Apple Hardware Test
so, i'm left with reinstalling os 10.5.x via install disk on my now erased / reformatted hard drive. after that, i'm going to try to (again) restore from the time machine disk (thank god all of my media and time machine backups are on separate hard disks...). Will a time machine restore into a freshly installed OS from a previous install?
Depends. A full restore, where you start from your Install disc, will erase the drive and restore everything, including OSX.
If you do an +Erase and Install+ of Leopard, then use +Setup Assistant+ (see #19 in Time Machine - Frequently Asked Questions (or use the link in *User Tips* at the top of this forum), it will bring over everything you select except OSX. Then download and instal the "combo" update to get back to 10.5.8. http://support.apple.com/downloads/MacOS_X_10_5_8_ComboUpdate Be sure to do a +Repair Permissions+ via Disk Utility (in your Applications/Utilities folder) afterwards.

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