Preferences reset upon restart

Hey all,
Been having some strange issues with Lion, or at least I think its Lion.. So here I am on my MacBook pro from 2010, reinstalling Snow Leopard and Lion afterwards. I install the updates and some programs (Plex, uTorrent, Chrome) only to realize that when I restart, some preferences completely ignored.. All programs added to the Dock are gone again, the assigned log-in items don't start up, iCloud was logged out again, mail settings were reset..
I reinstalled the whole thing, except for Lion, and it all worked fine. So anyway, I thought it was the laptop. Some sort of hardware problem or something, right? So I just got this new Mac mini, with Lion, and it does the same exact thing.
It doesn't remember some changes I made. I tried to repair permissions, but it doesn't do anything. Can anyone help me with this? Does anyone have seen the same problem?

Hi, I have only a tiny sub-set of these issues. But it started after I installed Lion. My issue is simply the auto-shutdown feature. I try to have this i-Mac shut down every day at 11 PM and restart at 6 AM. It worked perfectly with Snow Leopard. Sometimes it works, most of the time it doesn't. Some days I'll check on it early in the morning and it'll show the message that "This computer is shutting down X seconds". Today at 5 AM it was simply running with no messages, and probably had been running all night. I'd really like to get this feature to work. I've searched these boards and tried all the suggestions to no avail.

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