Marjolein,
They CAN be orthogonal, yes, IF you use an orthogonal design. Most researchers today opt for efficient designs, which compromise between pure orthogonality and pure level balance, two design criteria that are often in conflict. So the bottom line is that if you generate your design to achieve orthogonality, your alternative specific effects will be orthogonal, too, while if you generate your design to be efficient (possibly surrendering some orthogonality), your alternative specific effects will be part of that efficiency too (again, possibly surrendering some orthogonality).
