Windows Returning on Restart no matter what

Hi,
I have tried to fix this problem myself to no avail. I have the latest version of Lion on a Macbook Pro.
Whenever I restart the apps I had open always come back on, which is Safari and Mail. Safari opens with two tabs that I had open. This has been happening for about a week and a half now.
Whenever I shut down I have tried to uncheck the box on the dialog that says "Reopen windows when logging back in."
I have tried clearing my user caches, system caches, rebuilding permissions, even zap the pram. Nothing has worked. Safari and Mail keep opening when I start up. I have the Safari Restore extension installed for Safari to remember tabs that I had open and tried turning off extensions and restarting, but upon restart Safari automatically turns them back on.
Very frustrating.
Anyone have any ideas? Thanks.

It seems like this is a permissions issue, but I've rebuilt permissions a few times already.

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