Makerbot Rep. 2 - problems with first 3-4 layers

[Molleby]

I suspect that the model is not watertight as it is not normal for makerware to show anything but solid.

Well, the model prints normally and in good quality after the first 4 layers, so I don't think it is a question of that. I also tried to start a print with a raft, to see if that could take some of the bad layers. Result:

https://drive.google.com/file/d/0B6M...ew?usp=sharing
https://drive.google.com/file/d/0B6M...ew?usp=sharing

I'm beginning to think it might have something to do with over extrusion? And if it is over extrusion, how do I fix that?