Hi Steven,
Sorry for the delayed response but I have not been on the forum for a bit!
This plagued me for a long time but I finally worked out a solution using GI. I simply ticked "Generate shadow mask" on a floor plane and because this does not work with GI I added an area light at a very low intensity that casts the shadow and I get my item with a shadow on a transparent background. If you only want the shadow tick the item shadow object only.
Cheers,
Eric