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• Add "int accumOpacity" [1] to the PxrPathTracer integrator line in the rib file, or click accumOpacity checkbox in bridge tools.
• Make sure numIndirectSamples is greater than zero. If no indirect rays were created, all surface hits will be considered fully opaque.
• Make sure max path length maxPathLength in PxrPathTracer is set to be long enough for the camera paths to reach the end of your scene. For example, if you have 5 panes of glass and the max path is 1, the ray will not go through all the glass before it terminates and cannot generate the correct alpha values.  (Also make sure that the maxspeculardepth Attribute is set high enough.)
• Use or write a Bxdf that has a transmit lobe. Examples of such include PxrSurface, PxrLMGlass, etc.

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