Nope. And it is normal that the user store partitions - i.e. your documents - is left intact.
It's quite hard to guess what is wrong with your device. And since you sound a bit unsure whether Kubrick worked, I'm a bit unsure, too.
That said, I'm left puzzled. The symptoms you are facing don't sound the faintest bit like anything I've heard of before - and we have heard of many broken Kindles here in the dev' corner. If it is an option for you, I'd say contact Amazon and report it broken. As it is new, they should exchange it.
Also, in the back of my head I'm remembered of the thread that was talking about modifying the K3 refresh by parametrizing the e-ink driver. I don't remember it to be a permanent change, though. But it definitely had to do with modifying the contrast ratio.
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