If you allow me to make a suggestion about handout ... (hope so) Is it possible to fix the height of each slide on the handout page? If you have some picture or scheme constructed by rput (empty boxes for latex), when we try to make the handout the slide doesn't take into account such space. I have go through your package (again) a little bit to see how such minipage's are constructed and try to introduce the height on it, but is not easy ;)
I would suggest putting in a suitable \vspace to make space for the \rput. -Hendri.