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

Hi everybody

I have been having some problems recently with my Replicator 2. I am using firmware 7.6 and the latest version of Makerbot Desktop,

When I start a print, the first 3-4 layers are printed incorrectly. By that I mean, it seems like the build plate doesn't move enough along the z-axis, or that there is too much plastic coming out of the printer head. Either way, the nozzle scratches the top of the previous print layer and it looks bad. However, after the first 3-4 layers, everything begins to look normal and print quality is super fine. I've tried printing both from the SD card and from my computer. The threaded rod has been cleaned and re-lubricated.

Also, another weird thing... when I check the preview in Makerbot Desktop, the first 3 layers seems empty. Is that normal? Also, the red z-axis light stays on during the first 3 layers. Is that normal?

Here is an image of the first 4 layers, after which I cancelled the print (model is the default nuts and bolt):
https://drive.google.com/open?id=0B6...JBY0pQaFFiSmRV

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

Quote:

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Originally Posted by SHoutzager

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

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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?