Hope you forgive me if this is in the wrong place. I, like a lot of people uninstalled the extended prefs app. After this screwed the phone up, i copied over the Preferences (in the downloads section of mmif here). After doing this and restarting my phone I just had a blank space. I've just spent the last two hours trying to solve this problem and think i've come up with a working solution.

SSH in Phone/Applications/Preferences

check another iphone app like mobilecal or notes. Pay particular attention to the permissions. I noticed that all the .proj folders had 0755 permissions, the other files where all 0664 except the application file which is 0775. After restarting, all my settings are working again. Only weird thing is that I have a strange icon. A screwdriver crossed with a wrench. I hope this helps people. Anything but reinstalling stuff again eh.