Parenthesis not aligned with characters inside in arabic, using Xelatex

I re-ask the same question, more precisely...

I'm using Polyglossia to write a book of probability in arabic, and I've recently formatted my machine so I lost the last installation of fonts etc.. but not the files fortunately, saved periodically... So I have some problems for typesetting my old files, that I absolutely not understand... one problem what I never see it is that, after compilation, the parenthesis are behind the characters inside... and is really inacceptable when the main font is "Traditional Arabic", which is the font of the book (and still remains for another font... see example below)... This is the case for referred equation and for it's reference with different behaviour for two different fonts, and the same (bad) behaviour for text... See the words "(of null intersection)" This is also the case even if the characters used are Latin !!

My question is then: where do come from this problem?
how can I obtain centered parenthesis around the characters inside, for every font ?

Here is the basic tex file, of the same simple text, written with main font "Traditional arabic" first, and in the font Amiri, for watching the difference..

\documentclass[14pt,a4paper]{extbook}

\usepackage{amsmath,amssymb}
\usepackage{polyglossia}
\setmainlanguage[numerals=maghrib]{arabic}
\setotherlanguage{english}

\begin{document}
\LR{
Let  $E_{1}, E_{2},\ldots, E_{n}$, some disjoint events (of null intersection), then
$$%eqn3.1 \label{eqn3.1} P \left(\bigcup_{1}^{n} E_{i}\right) = \sum_{i = 1}^{n} P (E_{i})$$
The equation
\eqref{eqn3.1} generalizes to...
}

\vspace*{70pt}
\newfontfamily\arabicfont[Script=Arabic,Scale=1.2,AutoFakeSlant=-0.02]{Amiri}
\LR{
Let  $E_{1}, E_{2},\ldots, E_{n}$, some disjoint events (of null intersection), then
$$%eqn3.1 \label{eqn3.2} P \left(\bigcup_{1}^{n} E_{i}\right) = \sum_{i = 1}^{n} P (E_{i})$$
The equation
\eqref{eqn3.2} generalizes to...
}

\end{document}


And the result of my compilation (Using texmaker, and Windows 8)..

\LR{%
Let  $E_{1}, E_{2},\ldots, E_{n}$, some disjoint events (of null intersection), then
$$%eqn3.1 \label{eqn3.1} P \left(\bigcup_{1}^{n} E_{i}\right) = \sum_{i = 1}^{n} P (E_{i})$$