Your file runs good for me. However, some facts must be noticed from your MWE.
In your table you have used \begin{center} environment. This introduces some extra vertical place in the document. Use \centering instead.
Do not leave a blank line before and after the \figure or table environment. Instead put a comment line like this. This will avoid extra vertical space as latex will put a separate paragraph.

In figure or table environment, it is usually better not to put the placeholder like [!t]. Instead put [t] to give latex some room to adjust the placement. To keep the sections and figures/tables together you can use
\usepackage[section]{placeins}
so that they are placed within the respective sections. (use this package judiciously).
and somewhere in the first column of the last page, you say \balance to get columns balanced.
Note: If nothing works out and the problem persists, then you can avoid the figure/table environment (i.e., do not float them at all). Do
\usepackage{caption}
in your preamble and
{
\centering
\includegraphics[width=7cm]{images//user-code}
\captionof{figure}{caption}
\label{fig:user-code}
}
for figures and
{
\captionof{table}{caption}
\label{fig:user-code}
\centering
\begin{tabular}{| l | p{1.2cm} | l | }
\hline
\textbf{-} & \textbf{-} & \textbf{-} \\ \hline \hline
- & - & - \\ \hline
- & - & - \\ \hline
- & - & - \\ \hline
- & - & - \\ \hline
- & - & - \\ \hline
- & - & - \\ \hline
\end{tabular}
}
for tables. Hope this will be useful.

The last page with balanced columns:

Edit: OK now I managed to get the error with the file using the given ieeetran.cls.
The given ieeetran.cls is some how modified and is not compatible
with the package fixltx2e. Hence with the ieeetran.cls, fixltx2e
can not be used.
Given ieeetran.cls with fixltx2e gives this output:

and without fixltx2e (i.e., %\usepackage{fixltx2e} the output is:

I do not know how the ieeetran.cls provided by OP is modified and why? And how it changes this behavior is a mystery to me.
misalignment.texwith yourieeetran.clsthan with the CTAN version ofieeetran.cls. Does using the CTAN version fix your problem? Did you change anything in your version ofieeetran.cls? – Werner Mar 26 '12 at 6:52