Yes. The bumps on the opposite sides of the cube have to face the same direction.Does it have to do with the little bumps on the inner center piece?
The bumps are there to force the core to move with one side of the puzzle when you do a double-layer turn, so if you have bumps on both sides (which happens when they're not facing in the same direction), the cube will jam every time you try to do a double-layer turn.