Originally Posted by
FBinNY
The most likely suspect is a stiff link or an otherwise damaged link. Chain stretch can also be a factor, especially if either the chain or freewheel was replaced recently.
If all appears normal, measure your chain for stretch (search chain stretch here or the internet).
I know how to measure chain wear, and I know the chain's not worn, it's literally done about three or four miles, like the rest of the drivetrain. I'll check for stiff links, but I've had it skip twice in one turn of the cranks and then again on the next turn - I'd be surprised if a brand new Shimano chain had enough bad links in it to do that.