If I understand correctly, the question is how to create two copies of the presentation at the same time. To do this, you use several low-level tex commands and several files.
In Presentation.tex you may have
%&pdftex \relax \immediate\write18{pdflatex -synctex=1 PresentationWithBG.tex} \relax \immediate\write18{pdflatex -synctex=1 PresentationWithoutBG.tex} \end
This is the only file you really need to run latex on, what do you do with pdftex --shell-escape Presentation.tex . But you will also need the following.
In PresentationWithBG.tex (note that you really don't need \usebackgroundtemplate before each frame):
\documentclass{beamer} \setbeamercolor{background canvas}{bg=} \usebackgroundtemplate{\includegraphics[width=\paperwidth]{<your_background_fig>}} \input{PresentationContent}
In PresentationWithoutBG.tex :
\documentclass{beamer} \input{PresentationContent}
In PresentationContent.tex :
\begin{document} [All your actual presentation goes here...] \end{document}
When you run pdftex --shell-escape Presentation.tex , you will get PresentationWithBG.pdf and PresentationWithoutBG.pdf .
Please note that %&pdftex in Presentation.tex ensures that any version of TeX works in the correct mode. You could run it using pdflatex .
Mike
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