MDG,
I do not believe your story. For a couple of reasons.
1) I have been to a number of bakeries in America and none of them had a goy kneading the dough. In fact where I was, there were no non-jews working at all and one of the bakeries had yeshiva bochurim or regular chasidish women rolling, depending on the shift. And that is besides the kneading. So it is clear that not most use non jews.
2) I do not believe that the owner would tell you such a thing unless he thought you were a nudnik, which very well may be the case. Why would an owner pasul his own matzos.
The only place I could even fathom this beiing the case maybe that one year they baked in Romania a couple of years ago. However the large machine bakeries are mostly staffed by non-jews. I wonder which one has the kavanah lishmah.
S, either you made up your story out of whole cloth, or you are repeating as fact what someone was kidding you about.