I have a board with 5 through hole components (J1, J2, D6, D7, C5). In the 3D view, the two jumpers and the capacitor don’t have holes in the board for the grounded leg. The footprints are standard and both pads are specified as through hole. The cap (C5) for example is Capacitors_THT:CP_Radial_D6.3mm_P2.50mm.
Is this perhaps because there is a ground plane present on the top side running over the pad? Is the 3D view wrong and the hole will be included in the output files, or have I screwed something up?