The reduction weight of the internal points neighboring the outer boundaries is currently set in a "trapezoidal-rule" manner (1/2 on the box faces, 1/4 on the edges, 1/8 on the vertices, in 3D), regardless of the nature of the boundaries. In the case of periodic boundaries with a Coordbase::boundary_shiftout_* parameter of zero, this leads to the assignment of a non-zero weight to some of the boundary points. This only yields the correct result if boundary conditions have been applied, which sometimes isn't possible/necessary.
The attached patch introduces some logic in CarpetReduce to take care of this case. This may not be the best way to attack the problem though. One could tackle the way weight is assigned to zero-shiftout boundaries. Perhaps this issue is related to #1221.