Ah, well, that's what I needed to hear I think, that it has to be mechanical. Of course, immediately after a major overhaul I started looking for other explanations. And I do know that sometimes you can get a knock when pedaling if your stroke is weird. I had my cranks changed to shorter ones (which are so much better on my knees) and I was thinking maybe my stroke was causing it. Because it is so infrequent, I just cannot pinpoint it. A stiff link would be more consistent (not that I can find one). Every drivetrain part is brand new.
I'm going to call BF and I can Bart over to Warm Planet Bikes in the City (one of their dealers) to let them have a look. The bike wasn't shipped back, I got lucky and a friend picked it up and drove it back and BF packed it and put it in her car so if anything got messed up, it would be on them (everything looks aligned fine, though). Interestingly, yesterday it did NOT skip once but I only had time for 8 miles. Will see what happens today. Thanks everyone for all the suggestions!