Fonts are not rendering correctly

Question

I am using xelatex for printing Malayalam fonts. This is code and it is not printing properly. In the code it is right form and in the image that produced by the code is wrong

  \documentclass{article}
\usepackage[utf8]{inputenc}
\usepackage{fontspec}
\usepackage{polyglossia}
\setmainfont{Charis SIL}
\newfontfamily\Mal{Meera}

\begin{document}

\begin{table}
    \begin{tabular}{lllll}
    Case         & Marker                 & UF & SF & Gloss \\
    \hline
    Nominative   &  & ~  & ~ & \\
    Accusative   & -e \Mal{എ }\normalfont & \Mal{ആനയെ }\normalfont  & ~ & \\
    Dative       &   \Mal{ക്ക് }\normalfont                  & ~  & ~ & \\
    Instrumental &   \Mal{ആൽ  }\normalfont                & ~  & ~ & \\
    Locative     &  \Mal{ഇൽ }\normalfont             & ~  & ~ & \\
    Genitive     &  \Mal{ഉടെ, 
ഇന്റെ }\normalfont                    & ~  & ~ & \\
    Sociative    &  \Mal{ഓട് }\normalfont            & ~  & ~ & \\
        \hline
    \end{tabular}
\end{table}
\end{document}

You can easily identify the difference between code and output. Any suggestions ?

All the fonts are available here:

https://smc.org.in/fonts/
or


   http://www.prokerala.com/downloads/fonts.php

UPDATE

\usepackage{graphicx}
\usepackage{verbatim}
\usepackage{latexsym}
\usepackage{mathchars}
\usepackage{setspace}
\usepackage{amsmath}
\usepackage{fontspec}
}
\setmainfont[Mapping=tex-text]{Charis SIL}
\newfontfamily{\Mal}{Meera} [features=malayalam]


\input{blocked.sty}
\input{uhead.sty}
\input{boxit.sty}
\input{icthesis.sty}

\newcommand{\ipc}{{\sf ipc}}

\newcommand{\Prob}{\bbbp}
\newcommand{\Real}{\bbbr}
\newcommand{\real}{\Real}
\newcommand{\Int}{\bbbz}
\newcommand{\Nat}{\bbbn}

\newcommand{\NN}{{\sf I\kern-0.14emN}}   % Natural numbers
\newcommand{\ZZ}{{\sf Z\kern-0.45emZ}}   % Integers
\newcommand{\QQQ}{{\sf C\kern-0.48emQ}}   % Rational numbers
\newcommand{\RR}{{\sf I\kern-0.14emR}}   % Real numbers
\newcommand{\KK}{{\cal K}}
\newcommand{\OO}{{\cal O}}
\newcommand{\AAA}{{\bf A}}
\newcommand{\HH}{{\bf H}}
\newcommand{\II}{{\bf I}}
\newcommand{\LL}{{\bf L}}
\newcommand{\PP}{{\bf P}}
\newcommand{\PPprime}{{\bf P'}}
\newcommand{\QQ}{{\bf Q}}
\newcommand{\UU}{{\bf U}}
\newcommand{\UUprime}{{\bf U'}}
\newcommand{\zzero}{{\bf 0}}
\newcommand{\ppi}{\mbox{\boldmath $\pi$}}
\newcommand{\aalph}{\mbox{\boldmath $\alpha$}}
\newcommand{\bb}{{\bf b}}
\newcommand{\ee}{{\bf e}}
\newcommand{\mmu}{\mbox{\boldmath $\mu$}}
\newcommand{\vv}{{\bf v}}
\newcommand{\xx}{{\bf x}}
\newcommand{\yy}{{\bf y}}
\newcommand{\zz}{{\bf z}}
\newcommand{\oomeg}{\mbox{\boldmath $\omega$}}
\newcommand{\res}{{\bf res}}
\newcommand{\cchi}{{\mbox{\raisebox{.4ex}{$\chi$}}}}
%\newcommand{\cchi}{{\cal X}}
%\newcommand{\cchi}{\mbox{\Large $\chi$}}

% Logical operators and symbols
\newcommand{\imply}{\Rightarrow}
\newcommand{\bimply}{\Leftrightarrow}
\newcommand{\union}{\cup}
\newcommand{\intersect}{\cap}
\newcommand{\boolor}{\vee}
\newcommand{\booland}{\wedge}
\newcommand{\boolimply}{\imply}
\newcommand{\boolbimply}{\bimply}
\newcommand{\boolnot}{\neg}
\newcommand{\boolsat}{\!\models}
\newcommand{\boolnsat}{\!\not\models}


\newcommand{\op}[1]{\mathrm{#1}}
\newcommand{\s}[1]{\ensuremath{\mathcal #1}}

% Properly styled differentiation and integration operators
\newcommand{\diff}[1]{\mathrm{\frac{d}{d\mathit{#1}}}}
\newcommand{\diffII}[1]{\mathrm{\frac{d^2}{d\mathit{#1}^2}}}
\newcommand{\intg}[4]{\int_{#3}^{#4} #1 \, \mathrm{d}#2}
\newcommand{\intgd}[4]{\int\!\!\!\!\int_{#4} #1 \, \mathrm{d}#2 \, \mathrm{d}#3}

% Large () brackets on different lines of an eqnarray environment
\newcommand{\Leftbrace}[1]{\left(\raisebox{0mm}[#1][#1]{}\right.}
\newcommand{\Rightbrace}[1]{\left.\raisebox{0mm}[#1][#1]{}\right)}

% Funky symobols for footnotes
\newcommand{\symbolfootnote}{\renewcommand{\thefootnote}{\fnsymbol{footnote}}}
% now add \symbolfootnote to the beginning of the document...

\newcommand{\normallinespacing}{\renewcommand{\baselinestretch}{1.5} \normalsize}
\newcommand{\mediumlinespacing}{\renewcommand{\baselinestretch}{1.2} \normalsize}
\newcommand{\narrowlinespacing}{\renewcommand{\baselinestretch}{1.0} \normalsize}
\newcommand{\bump}{\noalign{\vspace*{\doublerulesep}}}
\newcommand{\cell}{\multicolumn{1}{}{}}
\newcommand{\spann}{\mbox{span}}
\newcommand{\diagg}{\mbox{diag}}
\newcommand{\modd}{\mbox{mod}}
\newcommand{\minn}{\mbox{min}}
\newcommand{\andd}{\mbox{and}}
\newcommand{\forr}{\mbox{for}}
\newcommand{\EE}{\mbox{E}}

\newcommand{\deff}{\stackrel{\mathrm{def}}{=}}
\newcommand{\syncc}{~\stackrel{\textstyle \rhd\kern-0.57em\lhd}{\scriptstyle L}~}

\def\coop{\mbox{\large $\rhd\!\!\!\lhd$}}
\newcommand{\sync}[1]{\raisebox{-1.0ex}{$\;\stackrel{\coop}{\scriptscriptstyle
#1}\,$}}

\newtheorem{definition}{Definition}[chapter]
\newtheorem{theorem}{Theorem}[chapter]

\newcommand{\Figref}[1]{Figure~\ref{#1}}
\newcommand{\fig}[3]{
 \begin{figure}[!ht]
 \begin{center}
 \scalebox{#3}{\includegraphics{figs/#1.ps}}
 \vspace{-0.1in}
 \caption[ ]{\label{#1} #2}
 \end{center}
 \end{figure}
}

\newcommand{\figtwo}[8]{
 \begin{figure}
 \parbox[b]{#4 \textwidth}{
 \begin{center}
 \scalebox{#3}{\includegraphics{figs/#1.ps}}
 \vspace{-0.1in}
 \caption{\label{#1}#2}
 \end{center}
 }
 \hfill
 \parbox[b]{#8 \textwidth}{
 \begin{center}
 \scalebox{#7}{\includegraphics{figs/#5.ps}}
 \vspace{-0.1in}
 \caption{\label{#5}#6}
 \end{center}
 }
 \end{figure}

}

All the code in the Header

UPDATE The problem caused because of older version of Texlive (2012). In Tex live 2015 there is no problem.