Do the WebGL effects have a detrimental impact on render cells? Render cells work best with static objects as I recall, but I'm not 100% certain how effects factor into things. Does the engine have to check effects every tick as it would an animation or event? There's no events tied to the shaders in question.
Recently discovered my big background full of static things actually had an effect applied that I forgot to remove, heh. Doesn't seem to muck with the performance, but better make sure before I let it live.