Because some plug-ins do not play well with Smart Filters we required specific info in the plug-in to be enabled for Smart Filter use.There should be a plug-in in your extras folder that will enable all plugins for Smart Filters – use at your own risk_
If you are into scripting you could create a script to run a filter on each frame. You could also record an action that runs the filter then advances to the next frame, which would still be slow, but at leats it would just be clicking paly on the action instead of a bunch of clicking for advance frame and run filter.
Mike Shaw
Photoshop QE