There's one sneaky way of accomplishing this, at least that I know of.
Instead of putting the logo on the master as a picture, add an image
control (View, Toolbars, check next to Control Toolbox, then click the
IMAGE control on the toolbox and put the control where you want it to
appear.)
Rightclick the control, choose Properties and set the Picture property
to the image you want to use (it needs to be BMP, JPG or WMF ... maybe
PNG depending on your version, not sure).
Experiment with PictureSizeMode to get it to show you the entire picture
w/o distortion. You might want to try ZOOM and set the size of the
control to something that's proportional to the size of the image you're
using.
When you go back to Normal view, it'll appear that it didn't work. Go
to the slide in Slide Show view and the logo will have popped to the
top.
If you need the thing to print properly ... well. Back to copy/pasting
the logo from the master to the slides where it's needed.
Oh, and while it works in slides shows in PPT itself, it won't work in
the free Viewer.