I agree with you, the only things that confuse me about Knox are (a) her strange behaviour during the initial stages of the investigation and (b) The fact that her parents have openly stated that if the appeal is succesful, they will pull her out of the country so that she, and they, can avoid a re-appeal as well as charges for slander from the Italian police for accusing them of coercion. That, to my mind, is not the behaviour of someone determined to prove their innocence, but will also readily agree that there is absolutely nothing there that is admissable in court as evidence.
The problem is, the hearing has been made into a show, it's more about the perception of Knox than the facts of the case. It's odd, because I was reading an American report claiming that Knox was being painted as an 'evil murderer' in the UK, which just goes to show all the more how media is defining this case, because whilst it is true that papers like The Mail have been acting as they usually do, I think most people in the UK are more interested in Justice for Meredith than putting Knox in jail, they just want whoever is guilty to be proved as such. Running away from the third appeal will do nothing but leave a pall of suspicioun over her.
Personally, I have a lot of questions over the evidence, but then, I also have a lot of questions over the behaviour of the suspect.