I have now fully uninstalled MiKTeX 2.7 and installed MiKTeX 2.8. Problem persists. Irritating.
It has something to do with the page layout not being interpreted correctly by pdftex, I think.
If I remove the a4paper option, I get two slides stacked on top of each other (the desired result), but the bottom slide cut off -- something wrong with both the size of the paper and the alignment of the slides on the paper.
To sum up, With I obtain: while with
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\usepackage{pgfpages}\pgfpagesuselayout{2 on 1}[a4paper]
I tried to force a specific papersize by setting things like the following in the preamble:
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\def\pgfpageoptionheight{12in}\def\pgfpageoptionheight{9in}
For reference, the pgfpages package defines the "2 on 1" layout as follows:
http://www.tex.ac.uk/tex-archive/graphi ... fpages.sty
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\pgfpagesdeclarelayout{2 on 1}{\edef\pgfpageoptionheight{\the\paperwidth} % landscaped by default\edef\pgfpageoptionwidth{\the\paperheight}\def\pgfpageoptionborder{0pt}\def\pgfpageoptionfirstshipout{1}}{\pgfpagesphysicalpageoptions{%logical pages=2,%physical height=\pgfpageoptionheight,%physical width=\pgfpageoptionwidth,%current logical shipout=\pgfpageoptionfirstshipout%}\ifdim\paperheight>\paperwidth\relax% put side-by-side\pgfpageslogicalpageoptions{1}{%border shrink=\pgfpageoptionborder,%resized width=.5\pgfphysicalwidth,%resized height=\pgfphysicalheight,%center=\pgfpoint{.25\pgfphysicalwidth}{.5\pgfphysicalheight}%}%\pgfpageslogicalpageoptions{2}{%border shrink=\pgfpageoptionborder,%resized width=.5\pgfphysicalwidth,%resized height=\pgfphysicalheight,%center=\pgfpoint{.75\pgfphysicalwidth}{.5\pgfphysicalheight}%}%\else% stack on top of one another\pgfpageslogicalpageoptions{1}{%border shrink=\pgfpageoptionborder,%resized width=\pgfphysicalwidth,%resized height=.5\pgfphysicalheight,%center=\pgfpoint{.5\pgfphysicalwidth}{.75\pgfphysicalheight}%}%\pgfpageslogicalpageoptions{2}