seems that mathtype doesn't parse a simple amsmath code or maybe the formula is too big to be processed by mathtype at once?

I want to create something like this in MS Word by MathType 6.9
The code that I'm using is:

\documentclass[a4paper]{book}
\usepackage{geometry}
\usepackage{amsmath}

\begin{document}

\begin{align}
  T_4 &= \langle \underline{k}\,.\,\underline{k}^{*^T} \rangle=
  \left\langle
  \begin{bmatrix}
  \left|k_1\right|^2 & k_1k_2^* & k_1k_3^* & k_1k_4^* \\
  k_2k_1^* & \left|k_2\right|^2 & k_2k_3^* & k_2k_4^* \\
  k_3k_1^* & k_3k_2^* & \left|k_3\right|^2 & k_3k_4^* \\
  k_4k_1^* & k_4k_2^* & k_4k_3^* & \left|k_4\right|^2
  \end{bmatrix}
  \right\rangle
  \\
  &=\frac{1}{2}
  \begin{aligned}[t]
  & \left[\begin{matrix}
  \langle|S_{XX}+S_{YY}|^2\rangle &
  \langle(S_{XX}+S_{YY})(S_{XX}-S_{YY})^*\rangle &\\
  \langle(S_{XX}-S_{YY})(S_{XX}+S_{YY})^*\rangle &
  \langle|S_{XX}-S_{YY}|^2\rangle & \cdots\cdots\\
  \langle(S_{XY}+S_{YX})(S_{XX}+S_{YY})^*\rangle&
  \langle(S_{XY}+S_{YX})(S_{XX}-S_{YY})^*\rangle & \cdots\cdots\\
  \langle j(S_{XY}-S_{YX})(S_{XX}+S_{YY})^*\rangle &
  \langle j(S_{XY}-S_{YX})(S_{XX}-S_{YY})^*\rangle &
  \end{matrix}\right.\\
  & \left.\begin{matrix}
  & \langle(S_{XX}+S_{YY})(S_{XY}+S_{YX})^*\rangle
  & \langle -j(S_{XX}+S_{YY})(S_{XY}-S_{YX})^*\rangle\\
  \cdots\cdots& \langle(S_{XX}-S_{YY})(S_{XY}+S_{YX})^*\rangle
  & \langle -j(S_{XX}-S_{YY})(S_{XY}-S_{YX})^*\rangle\\
  \cdots\cdots& \langle|S_{XY}+S_{YX}|^2\rangle
  & \langle-j(S_{XY}+S_{YX})(S_{XY}-S_{YX})^*\rangle\\
  & \langle j(S_{XY}-S_{YX})(S_{XY}+S_{YX})^*\rangle
  & \langle|S_{XY}-S_{YX}|^2\rangle
  \end{matrix}\right]
  \end{aligned}
\end{align}

\end{document}  

It's perfect when used in LaTeX and gives the following pdf result:

but unfortunately when I try to copy and paste the code between \begin{document} and \end{document} in MathType to create the same expression in word, I get the result:

It seems that MathType doesn't parse the codes \begin{aligned}[t] and \end{aligned} and as you know these are just amsmath packages code.
Do you know of any way -modifying the code or mathtype settings- to solve this problem?
Or do you have another suggestion to embed Latex equation into MS Word 2010?

Here is a toned-down version of your construction that doesn't use aligned:

\documentclass{article}
\usepackage[margin=1in]{geometry}% Just for this example
\usepackage{amsmath}

\begin{document}

\begin{align}
  T_4 &= \langle \underline{k}\,.\,\underline{k}^{*^T} \rangle=
    \left\langle
    \begin{bmatrix}
      |k_1|^2 & k_1k_2^* & k_1k_3^* & k_1k_4^* \\
      k_2k_1^* & |k_2|^2 & k_2k_3^* & k_2k_4^* \\
      k_3k_1^* & k_3k_2^* & |k_3|^2 & k_3k_4^* \\
      k_4k_1^* & k_4k_2^* & k_4k_3^* & |k_4|^2
    \end{bmatrix}
    \right\rangle \\
  &= \frac{1}{2}
    \left[\begin{matrix}
      \langle|S_{XX}+S_{YY}|^2\rangle &
      \langle(S_{XX}+S_{YY})(S_{XX}-S_{YY})^*\rangle &\\
      \langle(S_{XX}-S_{YY})(S_{XX}+S_{YY})^*\rangle &
      \langle|S_{XX}-S_{YY}|^2\rangle & \cdots\cdots\\
      \langle(S_{XY}+S_{YX})(S_{XX}+S_{YY})^*\rangle&
      \langle(S_{XY}+S_{YX})(S_{XX}-S_{YY})^*\rangle & \cdots\cdots\\
      \langle j(S_{XY}-S_{YX})(S_{XX}+S_{YY})^*\rangle &
      \langle j(S_{XY}-S_{YX})(S_{XX}-S_{YY})^*\rangle &
    \end{matrix}\right. \nonumber \\
  & \phantom{{}= \frac{1}{2}}
    \left.\begin{matrix}
      & \langle(S_{XX}+S_{YY})(S_{XY}+S_{YX})^*\rangle
      & \langle -j(S_{XX}+S_{YY})(S_{XY}-S_{YX})^*\rangle\\
      \cdots\cdots& \langle(S_{XX}-S_{YY})(S_{XY}+S_{YX})^*\rangle
      & \langle -j(S_{XX}-S_{YY})(S_{XY}-S_{YX})^*\rangle\\
      \cdots\cdots& \langle|S_{XY}+S_{YX}|^2\rangle
      & \langle-j(S_{XY}+S_{YX})(S_{XY}-S_{YX})^*\rangle\\
      & \langle j(S_{XY}-S_{YX})(S_{XY}+S_{YX})^*\rangle
      & \langle|S_{XY}-S_{YX}|^2\rangle
    \end{matrix}\right]
\end{align}

\end{document}

It's not possible to test this without access to MathType. So, while the above doesn't use aligned, you may have to remove some commands that are unknown to MathType.