MakerBot Industries

Does it look like that while its printing as well?

hmm. it's weird that it appears only in the first 5mm. I know it's a silly question.. but.. are you sure you don't have any obstacle (cable, piece of old raft, or something, that may be moved by the z-assembly) in the way of the y-axis that may "slow" it somehow down?

yet another more or less blind shot.. what about print temperature, flow rate and widht over thickness parameters? are they in the way that they push sufficient materal through the extruder? the idea why I ask is that I can imagine that if you extrude too little maybe too cold material it may not stick that well and be pulled in the wrong direction with the ongoing nozzle movement.
(Sorry if It's not good understandable.. but my English skills seems to be not sufficient to express myself in more clear way)

No, it's just a matter of settings when generating the gcode. That doesn't appear to be a mechanical error, and it's not a software bug,

Simply just not enough plastic being put down on each layer and since it's a circle, the layer pulls in from shrinkage. (As Yanisin described in his post) I imagine that part is pretty weak from the poor bonds between layers.
Quick fix is that when generating gcode using print-o-matic settings, go to the last tab of print o matic and change the diameter from 9.98 to something smaller like 8.98 or 7.98. Recently, in order to fix some similiar issues, I went as low as 6.6 diameter with no issues. This makes the software think it needs to turn the extruder motor more to get enough filament so it actually pushes more filament with a smaller number.

Tip of the day is that while using less plastic makes the part finish look better (like surface fill) it also makes very weak bonds between vertical layers and cause a whole host of other issues such as wierd problem like this. More palstic is better.
Also, reducing infill to 10% or less is advisable and helps limit heat retention, thus less warping a cracking of parts.

I'd say, try to decrease "infill perimeter overlap ratio" in fill module of skeinforge.

As I've posted before, you are using settings that are not optimal thus you have some print distortion.
#1 you shouldn't be using raft
#2 if your start height was correct, it would largly eliminate the issue
#3 decrease the pinch wheel diameter in print-o-matic to 8.89 or 7.89

Please post a picture of a print with those settings

Since the top layers are right, the ISSUE is flowrate and height settings period. The plastic is pulling inward on the lower layers due to being stretched as it layed down AKA your flowrate is slower than the feedrate.

sorry I have mk7 extruder so I'm not sure with the 3mm filament and mk6.
anyway.. what I have in my skeinforge is something like following (sorry, right now I'm not on the machine where I print):
layer height 0.35; perimeter width over thickness 1.6666 (-> 0.5 mm width); feed rate cca 26, flow rate: cca 2.8
I guess you still have incorrect combination of these parameters I just listed.
I'd try to set something similar to these ones.

Honestly I didn't manage to get used to the "print-o-matic settings" option in the window choosing the skeinforge profile after clicking on "generate g-code". You may have a problem there as well.