To get real transparency for box shadows with beamer, you could use this patch from the beamer repository. At this time, this patch is not included in beamer (see discussion).
If you use pdflatex, you can use the patched version of beamerbaseboxes.sty.
Here is the result of my MWE:

Here is the patched version of beamerbaseboxes.sty (put it in the same directory as your beamer document to get real transparency):
% Copyright 2003--2007 by Till Tantau
% Copyright 2010 by Vedran Mileti\'c
%
% This file may be distributed and/or modified
%
% 1. under the LaTeX Project Public License and/or
% 2. under the GNU Public License.
%
% See the file doc/licenses/LICENSE for more details.
\def\beamerboxesdeclarecolorscheme#1#2#3{% scheme name, upper color, lower color
\setbeamercolor{@scheme upper #1}{fg=white,bg={#2}}
\setbeamercolor{@scheme lower #1}{bg={#3}}
}
\define@key{beamerboxes}{scheme}{\def\bmb@upper{@scheme upper #1}\def\bmb@lower{@scheme lower #1}}
\define@key{beamerboxes}{upper}{\def\bmb@upper{#1}}
\define@key{beamerboxes}{lower}{\def\bmb@lower{#1}}
\define@key{beamerboxes}{width}{\edef\bmb@width{#1}}
\define@key{beamerboxes}{shadow}[true]{\csname bmb@shadow#1\endcsname}
\newif\ifbmb@shadow
\newbox\bmb@box
\newbox\bmb@colorbox
\newdimen\bmb@boxwidth
\newdimen\bmb@boxheight
\newdimen\bmb@prevheight
\newdimen\bmb@temp
\newdimen\bmb@dima
\newdimen\bmb@dimb
\newcommand\beamerboxesrounded[2][]{%
\global\let\beamer@firstlineitemizeunskip=\relax%
\vbox\bgroup%
\setkeys{beamerboxes}{upper=block title,lower=block body,width=\textwidth,shadow=false}%
\setkeys{beamerboxes}{#1}%
{%
\usebeamercolor{\bmb@lower}%
\globalcolorstrue%
\colorlet{lower.bg}{bg}%
}%
{%
\usebeamercolor{\bmb@upper}%
\globalcolorstrue%
\colorlet{upper.bg}{bg}%
}%
%
% Typeset head
%
\vskip4bp
\setbox\bmb@box=\hbox{%
\begin{minipage}[b]{\bmb@width}%
\usebeamercolor[fg]{\bmb@upper}%
#2%
\end{minipage}}%
\ifdim\wd\bmb@box=0pt%
\setbox\bmb@box=\hbox{}%
\ht\bmb@box=1.5pt%
\bmb@prevheight=-4.5pt%
\else%
\wd\bmb@box=\bmb@width%
\bmb@temp=\dp\bmb@box%
\ifdim\bmb@temp<1.5pt%
\bmb@temp=1.5pt%
\fi%
\setbox\bmb@box=\hbox{\raise\bmb@temp\hbox{\box\bmb@box}}%
\dp\bmb@box=0pt%
\bmb@prevheight=\ht\bmb@box%
\fi%
\bmb@temp=\bmb@width%
\bmb@dima=\bmb@temp\advance\bmb@dima by2.2bp%
\bmb@dimb=\bmb@temp\advance\bmb@dimb by4bp%
\hbox{%
\begin{pgfpicture}{0bp}{+-\ht\bmb@box}{0bp}{+-\ht\bmb@box}
\ifdim\wd\bmb@box=0pt%
\color{lower.bg}%
\else%
\color{upper.bg}%
\fi%
\pgfpathqmoveto{-4bp}{-1bp}
\pgfpathqcurveto{-4bp}{1.2bp}{-2.2bp}{3bp}{0bp}{3bp}
\pgfpathlineto{\pgfpoint{\bmb@temp}{3bp}}
\pgfpathcurveto%
{\pgfpoint{\bmb@dima}{3bp}}%
{\pgfpoint{\bmb@dimb}{1.2bp}}%
{\pgfpoint{\bmb@dimb}{-1bp}}%
\bmb@dima=-\ht\bmb@box%
\advance\bmb@dima by-2pt%
\pgfpathlineto{\pgfpoint{\bmb@dimb}{\bmb@dima}}
\pgfpathlineto{\pgfpoint{-4bp}{\bmb@dima}}
\pgfusepath{fill}
\end{pgfpicture}%
\copy\bmb@box%
}%
\nointerlineskip%
\vskip-1pt%
\ifdim\wd\bmb@box=0pt%
\else%
\hbox{%
\begin{pgfpicture}{0pt}{0pt}{\bmb@width}{6pt}
\bmb@dima=\bmb@width%
\advance\bmb@dima by8bp%
\pgfpathrectangle{\pgfpoint{-4bp}{-1bp}}{\pgfpoint{\bmb@dima}{8bp}}
\pgfusepath{clip}
{%
\pgftransformshift{\pgfpoint{-4bp}{0bp}}%
\pgftext[left,base]{\pgfuseshading{bmb@transition}}%
}%
\end{pgfpicture}%
}%
\nointerlineskip%
\vskip-0.5pt%
\fi%
\setbox\bmb@colorbox=\hbox{{\pgfpicturetrue\pgfsetcolor{lower.bg}}}%
\setbox\bmb@box=\hbox\bgroup\begin{minipage}[b]{\bmb@width}%
\vskip2pt%
\usebeamercolor[fg]{\bmb@lower}%
\colorlet{beamerstructure}{upper.bg}%
\colorlet{structure}{upper.bg}%
%\color{.}%
}
\def\endbeamerboxesrounded{%
\end{minipage}\egroup%
\bmb@temp=\dp\bmb@box%
\advance\bmb@temp by.5pt%
\setbox\bmb@box=\hbox{\raise\bmb@temp\hbox{\box\bmb@box}}%
\dp\bmb@box=0pt%
\bmb@boxwidth=\bmb@width%
\bmb@boxheight=\ht\bmb@box%
\advance\bmb@boxheight by4bp%
\advance\bmb@boxheight by\bmb@prevheight%
\ifbmb@shadow%
\pgfdeclareradialshading{bmb@shadowball}{\pgfpointorigin}
{%
color(0bp)=(pgftransparent!50);
color(4bp)=(pgftransparent!100)
}%
\pgfdeclareradialshading{bmb@shadowballlarge}{\pgfpointorigin}
{%
color(0bp)=(pgftransparent!0);
color(8bp)=(pgftransparent!100)
}%
\pgfdeclarehorizontalshading{bmb@shadowhorz}{\bmb@boxheight-6bp}
{%
color(0bp)=(pgftransparent!0);
color(8bp)=(pgftransparent!100)
}%
\pgfdeclareverticalshading{bmb@shadowvert}{\bmb@boxwidth-4bp}
{%
color(0bp)=(pgftransparent!100);
color(8bp)=(pgftransparent!0)
}%
\pgfdeclarefading{bmb@shadowmask}
{%
\begin{pgfpicture}
\pgftext[at=\pgfpoint{4bp}{4bp}]{\pgfuseshading{bmb@shadowball}}
\pgftext[at=\pgfpoint{\bmb@boxwidth}{8bp}]{\pgfuseshading{bmb@shadowballlarge}}
\pgftext[at=\pgfpoint{\bmb@boxwidth+4bp}{\bmb@boxheight+2bp}]{\pgfuseshading{bmb@shadowball}}
\pgftext[left, at=\pgfpoint{4bp}{4bp}]{\pgfuseshading{bmb@shadowvert}}
\pgftext[base, at=\pgfpoint{\bmb@boxwidth+4bp}{8bp}]{\pgfuseshading{bmb@shadowhorz}}
%
% clipping is needed because shadow is typeset on top of box
\begin{pgfscope}
\pgfsetcolor{black}
\pgfpathrectangle{\pgfpoint{4bp}{8bp}}{\pgfpoint{\bmb@boxwidth-0.2bp}{\bmb@boxheight-2bp}}
\pgfusepath{fill}
\end{pgfscope}
\end{pgfpicture}
}%
\fi%
\bmb@temp=\bmb@width%
\bmb@dima=\bmb@temp\advance\bmb@dima by2.2bp%
\bmb@dimb=\bmb@temp\advance\bmb@dimb by4bp%
\hbox{%
\begin{pgfpicture}{0bp}{0bp}{0bp}{0bp}
\ifbmb@shadow%
\begin{pgfscope}
\pgfpathrectangle{\pgfpoint{0bp}{-7bp}}
{\pgfpoint{\bmb@boxwidth+8bp}{\bmb@boxheight+6bp}}
\pgfsetfading{bmb@shadowmask}{%
\pgftransformshift{\pgfpoint{0.5\bmb@boxwidth+6bp}{0.5\bmb@boxheight-4bp}}}
\pgfusepath{fill}
\end{pgfscope}
\fi%
\unhbox\bmb@colorbox%
\pgfpathqmoveto{-4bp}{1bp}
\pgfpathqcurveto{-4bp}{-1.2bp}{-2.2bp}{-3bp}{0bp}{-3bp}
\pgfpathlineto{\pgfpoint{\the\bmb@temp}{-3bp}}
\pgfpathcurveto%
{\pgfpoint{\the\bmb@dima}{-3bp}}%
{\pgfpoint{\the\bmb@dimb}{-1.2bp}}%
{\pgfpoint{\the\bmb@dimb}{1bp}}%
{
\bmb@dima=\ht\bmb@box%
\pgfpathlineto{\pgfpoint{\bmb@dimb}{\bmb@dima}}
\pgfpathlineto{\pgfpoint{-4bp}{\bmb@dima}}
\pgfusepath{fill}
}
\end{pgfpicture}%
\box\bmb@box%
}%
\ifbmb@shadow%
\vskip4bp minus 2bp%
\else%
\vskip2bp%
\fi%
\egroup% of \vbox\bgroup
}
%
% Shadings
%
\pgfdeclareverticalshading[lower.bg,upper.bg]{bmb@transition}{200cm}%
{%
color(0pt)=(lower.bg);
color(2pt)=(lower.bg);
color(4pt)=(upper.bg)
}
beameroffered this feature for some time, but it is incompatible with the latex-dvips-ps2pdf route – Paul Gaborit Sep 25 '12 at 05:49