Upon checking I found that one of the stub point rails was interfering with the stock rail. Thus it wasn't closing properly. I nipped off about .0.020" and all was well. Even though the basement is heated and air conditioned, and the benchwork well seasoned in that room, I suppose the cold weather caused the benchwork to shrink more than the rail. Thus the rail had closed the gap. Hopefully as the temperature warms up the gap will not grow too wide.
Issues like this reinforce my decision to go for a simplified track plan with as few turnouts as possible to keep maintenance manageable.
On the bright side, the new boxcars do look good running on the layout.