The ToC inherits the color from your theme; the problem is that you are using
\tableofcontents[currentsection]
before the first \section command, so there's no current section to highlight, so all the information is shaded. Simply remove [currentsection]:
\documentclass[t,compress,11pt,xcolor=dvipsnames]{beamer}
\definecolor{LHCblue}{RGB}{4, 114, 255}
\usecolortheme[named=LHCblue]{structure}
\usepackage[bars]{beamerthemetree} %Beamer theme v 2.2
\usefonttheme[onlymath]{serif}
\usepackage{kerkis}
\setbeamercovered{higly dynamic}
\usetheme{Ilmenau} % Beamer theme v 3.0
\useoutertheme[subsection=true]{smoothbars}%Beamer Outer Theme-circles on top
\usefonttheme{serif}
\useinnertheme{circles} %rectangle bullet points instead of circle ones
\usepackage{beamerthemebars}
\setbeamerfont{section in toc}{size=\tiny}
\setbeamerfont{subsection in toc}{size=\tiny}
\title[Short Title]{Full Title}
\author{Author}
\institute{Institute}
\begin{document}
\begin{frame}
\titlepage
\end{frame}
\begin{frame}
\frametitle{Contents}
\tableofcontents
\end{frame}
\section{first section}
\begin{frame}
Intro to section
\end{frame}
\subsection{first subsection}
\begin{frame}
Theory
\end{frame}
\subsection{second subsection}
\begin{frame}
Experiment
\end{frame}
\subsection{third subsection}
\begin{frame}
Results
\end{frame}
\section{Back up slides}
\begin{frame}
1st Back up slide
\end{frame}
\begin{frame}
2nd Back up slide
\end{frame}
\begin{frame}
3rd Back up slide
\end{frame}
\end{document}

Or, setting the subsection in toc color, to use a shading of LHCblue:
\documentclass[t,compress,11pt,xcolor=dvipsnames]{beamer}
\definecolor{LHCblue}{RGB}{4, 114, 255}
\usecolortheme[named=LHCblue]{structure}
\usepackage[bars]{beamerthemetree} %Beamer theme v 2.2
\usefonttheme[onlymath]{serif}
\usepackage{kerkis}
\setbeamercovered{higly dynamic}
\usetheme{Ilmenau} % Beamer theme v 3.0
\useoutertheme[subsection=true]{smoothbars}%Beamer Outer Theme-circles on top
\usefonttheme{serif}
\useinnertheme{circles} %rectangle bullet points instead of circle ones
\usepackage{beamerthemebars}
\setbeamerfont{section in toc}{size=\tiny}
\setbeamerfont{subsection in toc}{size=\tiny}
\setbeamercolor{subsection in toc}{fg=LHCblue!40!black}
\title[Short Title]{Full Title}
\author{Author}
\institute{Institute}
\begin{document}
\begin{frame}
\titlepage
\end{frame}
\begin{frame}
\frametitle{Contents}
\tableofcontents
\end{frame}
\section{first section}
\begin{frame}
Intro to section
\end{frame}
\subsection{first subsection}
\begin{frame}
Theory
\end{frame}
\subsection{second subsection}
\begin{frame}
Experiment
\end{frame}
\subsection{third subsection}
\begin{frame}
Results
\end{frame}
\section{Back up slides}
\begin{frame}
1st Back up slide
\end{frame}
\begin{frame}
2nd Back up slide
\end{frame}
\begin{frame}
3rd Back up slide
\end{frame}
\end{document}

If you want table of contents at the beginning of each section, you can use something like
\AtBeginSection[]
{
\begin{frame}<beamer>
\frametitle{Outline}
\tableofcontents[currentsection]
\end{frame}
}
in the preamble.