Unfortunately that happens to me as well and it's not a setting. A work around that you can try is.. since it's a solid white space, you can use the PICK TOOL then select the MAGICWAND and click on the WHITE SPOT then just delete it. This will change the white back to transparent. Of course other members may have a better suggestions than this one.
I can't think of an easier way. The biggest issue with this is that if you have white areas inside the image you can't simply select the white area and delete it.
Smart Carver flattens your image leaving only 1 layer so it's not something you want to use on multiple layers. It does this because the result of using the smart carver tends to be that the image is resized.
Because of these two problems you also cannot make a selection of the transparency and save it out and reapply it because the image will then be a different size. And you cannot create a mask layer that will resize with the image to match up properly because it'll just merge down into the result.
However, the Smart Carver should really be one of the first filters you preform if you perform it at all. So the fact that you're starting with transparent areas suggests that you're doing the carving too late or on an image the smart carver was not designed to be used upon.
Might make it a wish for new versions to support maintaining layers and transparency.