This is actually the intended behaviour. Compare the description of \inserttotalframenumber and \insertpresentationendpage in the beamer manual (p. 66):
\inserttotalframenumber Inserts the total number of the frames (not slides) into a template. The number is only correct on the second run of TeX on your document.
vs.
\insertpresentationendpage Inserts the page number of the last page of the presentation (excluding
the appendix).
So \inserttotalframenumber counts the number of frames, which means it isn't increased in frames with overlays, while \insertpresentationendpage counts the absolute number of pages in the presentation, with each overlay as a single page.
What you're looking for instead is an \insertpresentationendframe command, which is unfortunately not available in beamer. However, you can define it yourself:
\def\insertpresentationendframe{\inserttotalframenumber}
\makeatletter
\g@addto@macro{\appendix}{\immediate\write\@auxout{\string\@writefile{nav}{\noexpand\headcommand{\noexpand\def\noexpand\insertpresentationendframe{\the\c@framenumber}}}}}
\makeatother
Insert this code into the preamble of your document, i. e. somewhere between \documentclass{beamer} and \begin{document}. It defines a macro \insertpresentationendframe which defaults to the total number of frames, but is "locked" to the number of the last frame of the main presentation if an appendix is encountered.
Using it is straightforward:
\documentclass{beamer}
\def\insertpresentationendframe{\inserttotalframenumber}
\makeatletter
\g@addto@macro{\appendix}{\immediate\write\@auxout{\string\@writefile{nav}{\noexpand\headcommand{\noexpand\def\noexpand\insertpresentationendframe{\the\c@framenumber}}}}}
\makeatother
\setbeamertemplate{footline}{\insertframenumber/\insertpresentationendframe}
\begin{document}
\begin{frame}
Slide one
\uncover<2>{still}
\end{frame}
\appendix
\begin{frame}
Slide two (appendix)
\end{frame}
\begin{frame}
Slide three (appendix)
\end{frame}
\end{document}
Observe that the frame counter now correctly shows 1/1 instead of 1/2.
20) and use\setbeamertemplate{footline}{\insertframenumber/20}. – Werner Dec 10 '11 at 20:36