I have tried all options and as it complains, you are simply using obsolete versions of the notes
option and make sure that you compile twice to be sure about the warnings. The cases below are fully working without any errors or warnings on Win7 64bit, Texniccenter 2 Alpha3, Miktex 2.9.
% 2. NOTES ON SEPARATE SLIDES:
\documentclass[show notes]{beamer}
% 3. NOTES ONLY:
\documentclass[show only notes]{beamer}
% 4. HANDOUTS:
\documentclass[handout,show notes]{beamer}
I have tried adding new sections and everything (hyperlinks etc.) looks working. I have used the example bibliography on page 102 of the manual (v.3.12) and it is also working without any errors and mistakes. Please edit your question further if you feel that there is still something that does not work.
Here is what I have used, just in case:
%% 1. DUAL-DISPLAY NOTES:
%\documentclass[
%hyperref={bookmarks=false}
%]{beamer}
%\usepackage{pgfpages}
%\setbeameroption{show notes on second screen=left}
% 2. NOTES ON SEPARATE SLIDES:
\documentclass[show notes]{beamer}
% 3. NOTES ONLY:
%\documentclass[show only notes]{beamer}
% 4. HANDOUTS:
%\documentclass[handout,show notes]{beamer}
% 5. NO NOTES: ONLY ONE THAT BUILDS WITHOUT WARNINGS
%\documentclass[hide notes]{beamer}
\mode<presentation>{
\usetheme{Warsaw}
\setbeamercovered{transparent}
}
\usepackage[latin1]{inputenc}
\usepackage{times}
\usepackage[T1]{fontenc}
\title[Pres\hspace{2em}\insertframenumber/
\inserttotalframenumber]{My Presentation}
\author[Me Me] {Me}
\institute[Univ.]{University}
\date[Sep. 14, 2011]{September 14$^{\text{th}}$, 2011}
% Makes TOC show at beginning og each section:
\AtBeginSubsection[]
{
\begin{frame}<beamer>{Outline}
\tableofcontents[currentsection,currentsubsection]
\end{frame}
\note{}
}
\begin{document}
\begin{frame}
\titlepage
\end{frame}
\note{}
\begin{frame}{Outline}
\tableofcontents
\end{frame}
\note{}
\section{Introduction}
\begin{frame}{A content frame }
\begin{itemize}[<+->]
\item Here is some content.
\note[item]{And here is a related note.}
\item More content.
\note[item]{Another note. }
\item Yet more content.
\note[item]{Yet again a note.}
\end{itemize}
\end{frame}
\begin{frame}{A second content frame}
\begin{itemize}
\uncover<1->{
\item Indented content:
\begin{itemize}
\item First piece.
\note[item]<1->{Note about first piece. }
\end{itemize}
}
\uncover<2->{
\item More content.
\begin{itemize}
\item More indented content.
\note[item]<2-> {Note about this second piece of content. }
}
\end{itemize}
\end{itemize}
\end{frame}
\section{Section 2}
\begin{frame}
\begin{block}{citation}it cites \cite{Salomaa1973}\end{block}
\end{frame}
\subsection{Subsection1}
\begin{frame}
\begin{block}{block1}content 1\end{block}
\end{frame}
\subsection{Subsection2}
\begin{frame}
\begin{block}{block 2}content 2\end{block}
\end{frame}
\begin{frame}
\begin{thebibliography}{Dijkstra, 1982}
\bibitem[Salomaa, 1973]{Salomaa1973}
A.~Salomaa.
\newblock {\em Formal Languages}.
\newblock Academic Press, 1973.
\bibitem[Dijkstra, 1982]{Dijkstra1982}
E.~Dijkstra.
102
\newblock Smoothsort, an alternative for sorting in situ.
\newblock {\em Science of Computer Programming}, 1(3):223--233, 1982.
\end{thebibliography}
\end{frame}
\end{document}
EDIT: It turns out that I did not try it with option 1 afterwards. I was able to reproduce the warnings. I will try to see if I can come up with something.
EDIT2: I have switched the location of the presentation and the notes and at least it works as it should. The problem I am guessing is that hyperref only defines hyperlinks for the part on the left and then when creating that small minipage at the corner of the notes, it gets confused since they are defined already on the body of the presentation.
\documentclass[hyperref={bookmarks=false}]{beamer}
\usepackage{pgfpages}
\setbeameroption{show notes on second screen=left}
this still gives you the warning but the presentation works fine.
Frankfurt
uses the smoothbars
outer theme which sets the headline
template but doesn't set the footline
template. To change the header position to the bottom of the frame, it's enough to set the footline
template to behave exactly as smoothbars
sets the headline template. To place the navigation symbols in the header, you need to redefine the navigation symbols
template to do nothing and then to insert the symbols in the headline
template:
\documentclass{beamer}
\usetheme{Frankfurt}
\setbeamertemplate{navigation symbols}{}
\makeatletter
\setbeamertemplate{footline}
{%
\pgfuseshading{beamer@barshade}%
\ifbeamer@sb@subsection%
\vskip-9.75ex%
\else%
\vskip-7ex%
\fi%
\begin{beamercolorbox}[ignorebg,ht=2.25ex,dp=3.75ex]{section in head/foot}
\insertnavigation{\paperwidth}
\end{beamercolorbox}%
\ifbeamer@sb@subsection%
\begin{beamercolorbox}[ignorebg,ht=2.125ex,dp=1.125ex,%
leftskip=.3cm,rightskip=.3cm plus1fil]{subsection in head/foot}
\usebeamerfont{subsection in head/foot}\insertsubsectionhead
\end{beamercolorbox}%
\fi%
}%
\setbeamertemplate{headline}{%
\hskip1em\usebeamercolor[fg]{navigation symbols dimmed}%
\insertslidenavigationsymbol%
\insertframenavigationsymbol%
\insertsectionnavigationsymbol%
\insertsubsectionnavigationsymbol%
\insertdocnavigationsymbol%
\insertbackfindforwardnavigationsymbol%
}
\makeatother
\begin{document}
\section{Test section}
\subsection{Test subsection one}
\begin{frame}Test\end{frame}
\subsection{Test subsection two}
\begin{frame}Test\end{frame}
\end{document}
Best Answer
Possibility 1:
Use Beamers build in navigation
Possibility 2:
Put your buttons in the footline