it looks like your y axis may be binding and skipping steps.
Follow this guide if you haven't already.
http://vimeo.com/55031028
What i do to check my axis setup is move the printer head to the extream X and Y with the 100mm step button on the manual control. If it skips during rapid motion, then i dont' have it set correctly. So I go back and re-align everything and adjust belts. You will know if it's skipping because it makes a horrible noise.
I've found the SD3 to be pretty sensitive to being crashed. I had a filament bind up while i was away from the printer and I had to re-do Y-axis adjustment. then I had to go back and adjust my steps in the firmware. I've been printing pretty steady for about a week now. Mainly printing out my replacement parts and the printer has been performing very well. I changed from black to red filament a few days ago and I still have some settings i need to tweak for thin/single wall prints, but so far, the solid prints are doing very well. Maybe it's because I started with black filament, but it seemed it was way easier to get dialed in.
Good luck