Damn you Caramdir, four minutes too late!
Anyway, here's what I came up with. Caramdir's is at least as good, but mine is a bit closer to your syntax, maybe...
\documentclass[english,ignorenonframetext,table]{beamer}
\usepackage[T1]{fontenc}
\usepackage[latin9]{inputenc}
\setcounter{secnumdepth}{3}
\setcounter{tocdepth}{3}
\usepackage{graphicx}
\makeatletter
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% LyX specific LaTeX commands.
%% A simple dot to overcome graphicx limitations
\newcommand{\lyxdot}{.}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Textclass specific LaTeX commands.
% this default might be overridden by plain title style
\newcommand\makebeamertitle{\frame{\maketitle}}%
\AtBeginDocument{
\let\origtableofcontents=\tableofcontents
\def\tableofcontents{\@ifnextchar[{\origtableofcontents}{\gobbletableofcontents}}
\def\gobbletableofcontents#1{\origtableofcontents}
}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% User specified LaTeX commands.
\usepackage{xcolor}
\usepackage{listings}
\usetheme{Frankfurt} %Warsaw
\usecolortheme{albatross}
\setbeamercovered{transparent}
\newcommand{\tformating}{
\definecolor{darkPurple}{rgb}{0.101960784313725,0,0.2}
\definecolor{purple}{rgb}{0.2,0,0.4}
\definecolor{lightPurple}{rgb}{0.4,0,0.4}
\rowcolors[]{1}{darkPurple}{purple}
\small
}
\usepackage{tikz,overpic}
\usetikzlibrary{fit,shapes.misc}
\makeatother
\usepackage{babel}
\begin{document}
\begin{frame}
\frametitle{ESR1}
\begin{center}
Functional analysis
\par\end{center}
\begin{center}
\only<1>{\begin{overpic}[width=1\textheight]{some_image.jpg}
\end{overpic}}%
\only<2>{\begin{overpic}[width=1\textheight]{some_image.jpg}
\put(40,38){\tikz \draw[red,thick,rounded corners] (0,0) rectangle (5,1.2);}
\end{overpic}}%
\only<3>{\begin{overpic}[width=1\textheight]{some_image.jpg}
\put(40,38){\tikz \draw[red,thick,rounded corners] (0,0) rectangle (5,1.2);}
\put(0,14){\tikz \draw[red,thick,rounded corners] (0,0) rectangle (3.5,1.2);}
\end{overpic}}%
\par\end{center}
\end{frame}
\end{document}
