System and Finder Preferences not saving

I'm very frustrated with OS X Lion.

First I hate the app windows in my face when I first start up my computer. There is a reason I quit them and shut off my computer. I don't want to see them every time I turn on my computer.

It's easy to shut off? Just go into system prefrences and uncheck "Restore Windows when quitting and re-opening apps". Easy except for one minor detail. My system preferences don't save. I uncheck it and restart guess what? It's checked again.

Preferences saving is not limited to the System prefereneces though. The finder and all my app preferences are not able to be saved either.

This is very frustrating.