Unfortunately my glsl knowledge is second to none so I can only help you based on the documentation available here and there. It seems Qt has nothing to do with this and the problem is only in the configuration of the environment. Since shader programs are tied to a specific GL context, maybe the problem is that you didn't initialize the context properly? To use multitexturing, you have to enable multiple texturing units first. In pure OpenGL this is done with something similar to:
glActiveTextureARB(GL_TEXTURE0_ARB);
glEnable(GL_TEXTURE_2D);
glActiveTextureARB(GL_TEXTURE1_ARB);
glEnable(GL_TEXTURE_1D);
glActiveTextureARB(GL_TEXTURE0_ARB);
glEnable(GL_TEXTURE_2D);
glActiveTextureARB(GL_TEXTURE1_ARB);
glEnable(GL_TEXTURE_1D);
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Do you have something like that when your context is initialized? Note, this is all just a guess.
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