seems like shake is rendering out the alpha (if render 16 bit) by default.
in shake, its better to give every clip alpha (turn auto alpha on if no alpha), say if your bkg got no alpha ( full frame), and your layers got alpha, then when render to fcp, the clip will have alpha of the layers. So, your bkg will have hole in it (it suppose to be full frame).
in fcp, you can set alpha to ignore to get the full frame. or to black or straight to get back the alpha
thanks