The problem is, that my shader setup works differently depending on what shader I run before. If I run
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GX_SetTevOrder(GX_TEVSTAGE0, GX_TEXCOORD1, GX_TEXMAP1, GX_COLOR0A0);
initQuad(); // vertex setup
drawQuad(1.0f); // draw a single quad with 4 vertices, I assume that is required because state is not written until a GX_Begin()
My shader uses
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GX_SetTevOrder(GX_TEVSTAGE0, GX_TEXCOORD2, GX_TEXMAP_NULL, GX_COLORZERO);