I can not see any problem here. I guess that some problem with encoding or end of line could be the reason.
See the image.

The code.
\documentclass[11pt,a4paper]{report}
\usepackage[latin1]{inputenc}
\usepackage{amsmath}
\begin{document}
\[J_{i} = \begin{bmatrix}%
x_{i} & 1 & 0 & \cdots & 0 & | & 0 & 0 & 0 & \cdots & 0 & & \cdots \\%
%0 & x_{i} & 1 & \cdots & 0 & | & 0 & 0 & 0 & \cdots & 0 & & \cdots \\
%\vdots & \vdots & \vdots & \ddots & \vdots & | & \vdots & \vdots & \vdots & \ddots & \vdots & & \cdots \\
%0 & 0 & 0 & \cdots & 1 & | & 0 & 0 & 0 & \cdots & 0 & & \cdots \\
%0 & 0 & 0 & \cdots & x_{i} & | & 0 & 0 & 0 & \cdots & 0 & & \cdots \\
%- & - & - & - - - & - & - & - & - & - & - - - & - & & \\
%0 & 0 & 0 & \cdots & 0 & | & x_{i} & 1 & 0 & \cdots & 0 & & \cdots \\
%0 & 0 & 0 & \cdots & 0 & | & 0 & x_{i} & 1 & \cdots & 0 & & \cdots \\
%\vdots & \vdots & \vdots & \ddots & \vdots & | & \vdots & \vdots & \vdots & \ddots & \vdots & & \cdots \\
%0 & 0 & 0 & \cdots & 0 & | & 0 & 0 & 0 & \cdots & 1 & & \cdots \\
%0 & 0 & 0 & \cdots & 0 & | & 0 & 0 & 0 & \cdots & x_{i} & & \cdots \\
%- & - & - & - - - & - & - & - & - & - & - - - & - & & \\
%\vdots & \vdots & \vdots & \vdots & \vdots & & \vdots & \vdots & \vdots & \vdots & \vdots & & \ddots
\end{bmatrix}
\]
\end{document}
\bmatrix? – Werner Mar 17 '14 at 16:08