In Snap Art 1, when a filter is run on a layer with transparency, the background remains transparent. In Snap Art 2, the behavior was changed so the canvas is always revealed at 100% opacity under the transparent pixels.

If you want the old behavior you can create a layer mask before you run the filter. To do so, control click (command click on the Mac) the layer with the opacity (the image in the layers palette). This will load a selection of the opaque pixels. Then click the add layer mask icon at the bottom of the layers palette (looks like a rectangle with a circle in it). This creates the layer mask. Then click the image in the layer palette again (since the mask is selected). Now when you run the effect in Snap Art your effect will be masked out.

Yet another approach is to run the filter on the desired layer, making sure the "Create Output on New Layer" option is checked. Then in the Layers Palette, select the original layer and Control or Command click the layer icon to make it a selection. Then in the new output layer just choose select inverse and hit the delete key.