Clipping is done by replacing a shader. NGUI comes with an assortment of shaders, such as the default one Unlit - Transparent Colored. Note how it has several versions, such as Unlit - Transparent Colored 1, 2, etc? Each one represents how many times it gets clipped. Assuming you wrote a custom shader, you also need to write a custom clipped shader for it in order for clipping to work. Use NGUI's shaders as an example.
