Alright, so lets describe the more important problem first. No functionality after login.
I guess I could go a bit easier on this, I've reinstalled ubuntu 3 times now, running 12.10 and I have had this issue 3 times now, granted it was always after an update of some sort, usually the NVidia driver I believe.

I login and the desktop appears, my icons are there and everything, now the bar up top is no longer visible and the bar to the left is also gone, when i try to do anything typing wise, a text field opens at the bottom right of the screen, but I've yet to get any command functionality from it, I have yet to get much functionality from hotkeys aswell, usually when I pull up the terminal Ubuntu freezes (ALT+CTRL+F1-6 work fine)

When i do get hotkeys to bring up windows, none of them take priority over the others (OnTop) -- THey are just drawn in an array it seems and the last one drawn is on top, permanatly.

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HDMI Problem -- Screen doesn't even register most of the time, although when it does it just sits there with a purple ubuntu screen. Like it's loading. Can't get anything else from it.