Prusa i2 print issues

Hi all,
My first post here.I have been following this forum for sometime now. I just completed my prusa, and after some basic calibrations I was getting decent prints. I am using a sanguinololu board with sprinter firmware, with no heatbed.

Recently after upgrading the pronterface software (along with slic3r) I am having this weird issue. The second layer is not matching the base layer, it is getting shifted .Initially it was random, but now it appears to happen with every print.I have no idea how to debug this issue.

Another minor issue: Any idea how to get rid of this unevenness shown here . The extruder appears to pause very briefly before starting a new layer extruding little extra filament.


Please let me know if anyone has any suggestions.

Thanks in advance.

I had that happen, drove me nuts, then I found my problem. My heat bed wires would get caught on the clips for the glass, and slide the glass off, then it would move itself back and un hook itself from the clip. I saw it happen one day, and moved my wires. The funny thing is once it starts "shifting" it can get caught on filament balls, burn them, and send the print shifting every few layers until I have a 4 hour mess of solid shifts.