problems restoring from time machine

So my late model macbook pro started having some strange issues then wouldn't even boot into my mac partition, only the windows side. So i popped in my snow leopard CD and restored from my time machine backup. All my files seem to have been restored but lots of things like preferences, settings in apps, bookmarks, my background and dock settings, and other stuff like that weren't put back to normal. I thought time machine was supposed to keep all my preferences and stuff? Did something go wrong or did I just expect too much?
Thanks!

When you selected to restore from time machine backups, you would have been asked if you want restore files and folders, applications, user settings and preferences, etc.
You may have chosen not to restore your user settings my mistake.

I've tried again and can't seem to find that option. I am using snow leopard install disks if that matters? I feel like i remember there being more options on leopard install disks.