File Vault lost my preferences

Hi guys. For the heck of it I decided to turn on my File Vault which, if I'm not mistaken, encrypts the contents of your home folder. After doing that it logged me out while encrypting, and then let me log back in. When I did, all of my preferences, browser bookmarks, extra dock items, etc. disappeared. In addition to that, all of my applications launch like it was the first time and the only items left in my home folder are Desktop, Documents (which is EMPTY—Lord help me if all of that info is lost) and Library. I decided to turn File Vault off and even restarted, but all of my old settings seem to be gone. Any ideas what happened to them and how I can get these valuable preferences and documents restored. The way the computer is behaving is as if I had created a new user. There is only one user on my machine—me, and I have full admin privileges. Would repairing permissions help, or would I be cementing myself here forever. I really don't want to tweak around too much until I hear if this is common with an easy fix. ANY help would be appreciated. I swear, I'll name my firstborn iPod for whomever among you can offer some suggestions to restore my system the way it used to be. Thanks!

G4 Dual 550 Mac OS X (10.4.8) 1.2 GB RAM, 380 GB Storage, DVD Burner/Handy Slide-Out Cup Holder, USB2, TV Tune

G4 Dual 550 Mac OS X (10.4.8) 1.2 GB RAM, 380 GB Storage, DVD Burner/Handy Slide-Out Cup Holder, USB2, TV Tune