I have a particle system on all of my cannons in my game. The particle system uses a specific shader but whenever the cannon is instantiated from the script the shader changes to a default one. If I drag the prefab into the game world, even during run time, it'll have the correct shader. But when a script calls Resources.Load to bring the cannon in, the shader used for the material in the particle system resets.
When the object is dragged in: http://imgur.com/R1wGTJI
When it's instantiated: http://imgur.com/1dEMn0i
Have you compared the rest of the settings of your particle system that it is instantiated from the intended prefab? Otherwise you may reproduce the bug in a much simpler scene with minimal assets involved and then file a bug ticket to Unity.
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