I agree that the pinning can be the problem, but I'd also recommend using a walking foot. Then there is no "pushing" of the top fabric forward knocking the seams off center. Personally, I don't use pins unless absolutely necessary. I prefer the method of starting the first part, then holding the joining area until it goes under the needle, then lining up the last part of the seam. But that's just me. I think it's mostly because I stab myself with pins a lot, and sometimes forget to take them out before driving over them - breaking both pins and needles in the process.
