Using the acolumns environment from this question I discovered that the horizontal alignment of the columns is modified in same way.
I'm using it for a poster and the difference becomes quite notable.
This example should show the vertical misalignment between blocks
\documentclass{beamer}
\usecolortheme{rose}
\usepackage{environ}% Required for \NewEnviron, i.e. to read the whole body of the environment
\makeatletter
\newcounter{acolumn}% Number of current column
\newlength{\acolumnmaxheight}% Maximum column height
% `column` replacement to measure height
\newenvironment{@acolumn}[1]{%
\stepcounter{acolumn}%
\begin{lrbox}{\@tempboxa}%
\begin{minipage}{#1}%
}{%
\end{minipage}
\end{lrbox}
\@tempdimc=\dimexpr\ht\@tempboxa+\dp\@tempboxa\relax
% Save height of this column:
\expandafter\xdef\csname acolumn@height@\roman{acolumn}\endcsname{\the\@tempdimc}%
% Save maximum height
\ifdim\@tempdimc>\acolumnmaxheight
\global\acolumnmaxheight=\@tempdimc
\fi
}
% `column` wrapper which sets the height beforehand
\newenvironment{@@acolumn}[1]{%
\stepcounter{acolumn}%
% The \autoheight macro contains a \vspace macro with the maximum height minus the natural column height
\edef\autoheight{\noexpand\vspace*{\dimexpr\acolumnmaxheight-\csname acolumn@height@\roman{acolumn}\endcsname\relax}}%
% Call original `column`:
\begin{orig@column}{#1}%
}{%
\end{orig@column}%
}
% Save orignal `column` environment away
\let\orig@column\column
\let\endorig@column\endcolumn
% `columns` variant with automatic height adjustment
\NewEnviron{acolumns}[1][]{%
% Init vars:
\setcounter{acolumn}{0}%
\setlength{\acolumnmaxheight}{0pt}%
\def\autoheight{\vspace*{0pt}}%
% Set `column` environment to special measuring environment
\let\column\@acolumn
\let\endcolumn\end@acolumn
\BODY% measure heights
% Reset counter for second processing round
\setcounter{acolumn}{0}%
% Set `column` environment to wrapper
\let\column\@@acolumn
\let\endcolumn\end@@acolumn
% Finally process columns now for real
\begin{columns}[#1]%
\BODY
\end{columns}%
}
\makeatother
\begin{document}
\begin{frame}{A frame}
\begin{acolumns}[t]
\begin{column}{0.5\linewidth}
\begin{block}{A block}
Hello
\autoheight
\end{block}
\end{column}
\begin{column}{0.5\linewidth}
\begin{block}{Another block}
This one has a larger height since it has an itemize
\begin{itemize}
\item item a
\end{itemize}
\autoheight
\end{block}
\end{column}
\end{acolumns}
\begin{columns}[t]
\begin{column}{0.5\linewidth}
\begin{block}{A block}
Hello
\end{block}
\end{column}
\begin{column}{0.5\linewidth}
\begin{block}{Another block}
This one has a larger height since it has an itemize
\begin{itemize}
\item item a
\end{itemize}
\end{block}
\end{column}
\end{columns}
\end{frame}
\end{document}
is there some spurious space that introduces it?
EDIT
add
\usepackage{tikz}
%...
\tikz[remember picture,overlay] \draw [red,xshift=1em] (current page.north west) ++(1em,0) |- (current page.south west);
at the end of the frame to better see the misalignment.

upper left block crosses the red line, bottom one doesn't!
\end{minipage}%<< \end{lrbox}%<<but I couldn't work out where you are seeing the bad alignment so I don't know if this fixes anything – David Carlisle May 04 '12 at 16:08%on line 74:end{column}%the horizontal alignment seems fine. Is this what you are referring to? – Peter Grill May 04 '12 at 16:27%only for theacolumnsenvironment? where's the spurious space? – capitalaslash May 04 '12 at 17:13%s but they don't solve the issue. see question update that shows better the problem – capitalaslash May 04 '12 at 17:30