Finally it seems to not come from the empty geode. The origin of the problem seems to be the uniform initialization during the building of the program which call a glUseProgram.
If your scene never display the node that contains the shader and if there is no other shader on the scene, this "glUseProgram" is the only one that is called during your simulation. So, this shader is applied on all the scene.
I fix this bug by switching off the shader (by calling glUseProgram(0) ) during the compilation of a state which does not contain the shader.
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