This periodic mesh should work

examples/cube/cube_periodic.json

@@ -40,12 +40,12 @@
   {
     "Periodic":
     {
-      "OriginalAttributes": [1, 2],
-      "DuplicateAttributes": [6, 4]
+      "OriginalAttributes": [3, 5],
+      "DuplicateAttributes": [4, 6]
     },
     "PEC":
     {
-      "Attributes": [3, 5]
+      "Attributes": [1, 2]
     }
   },
   "Solver":

examples/cube/mesh/cube_periodic.geo

@@ -0,0 +1,38 @@
+// Periodic hexahedral cube mesh
+
+Point(1) = {0, 0, 0, 1.0};
+Point(2) = {1, 0, 0, 1.0};
+Point(3) = {1, 1, 0, 1.0};
+Point(4) = {0, 1, 0, 1.0};
+
+Characteristic Length {:} = 0.25;
+
+Line(1) = {1, 2};
+Line(2) = {2, 3};
+Line(3) = {3, 4};
+Line(4) = {4, 1};
+
+//Periodic Curve {1} = {-3};
+//Periodic Curve {2} = {-4};
+
+Curve Loop(1) = {1, 2, 3, 4};
+Plane Surface(1) = {1};
+Transfinite Surface {1};
+
+Recombine Surface {1};
+out[] = Extrude {0, 0, 1} { Surface{1}; Layers{4}; Recombine; };
+
+Physical Volume(1) = {out[1]};
+Physical Surface(1) = {1};      // back
+Physical Surface(2) = {out[5]}; // front
+Physical Surface(3) = {out[4]}; // left
+Physical Surface(4) = {out[2]}; // right
+Physical Surface(5) = {out[0]}; // bottom
+Physical Surface(6) = {out[3]}; // top
+
+Mesh 3;
+Mesh.MshFileVersion = 2.2;
+
+//Periodic Surface {out[0]} = {1} Translate {0, 0, 1}; // No periodicity in the z-direction (back & front)
+Periodic Surface {out[4]} = {out[2]} Translate {0, 1, 0}; // left and right
+Periodic Surface {out[3]} = {out[5]} Translate {1, 0, 0}; // bottom and top