You've not given us much go to on. Nevertheless I'm going to go out on a limb here and make some guesses about what might be going on.
According to your comments, the height of the two images is the same. In that case, there's nothing in your partial example that should result in misaligned images. Here's your partial example built into a MWE as follows
\documentclass{article}
\usepackage[margin=1in]{geometry}
\usepackage[demo]{graphicx}
\usepackage{subfigure}
\pagestyle{empty}
\usepackage{lipsum}
\begin{document}
\lipsum[1]
\begin{figure*}
\begin{minipage}[b]{2.5in}
\centering
\includegraphics[width=2.28in]{P}
\caption{P is a figure.}
\label{figure:p}
\end{minipage}
\hspace{0.21in}
\begin{minipage}[b]{2.5in}
\centering
\includegraphics[width=2.28in]{D}
\caption{D is a figure.}
\label{figure:d}
\end{minipage}
\end{figure*}
\lipsum[2]
\end{document}

A possible issue might be that the contents of the caption might have different heights and depths. Here's a rather extreme example of what I'm referring to:
\documentclass{article}
\usepackage[margin=1in]{geometry}
\usepackage[demo]{graphicx}
\usepackage{subfigure}
\pagestyle{empty}
\usepackage{lipsum}
\begin{document}
\lipsum[1]
\begin{figure*}
\begin{minipage}[b]{2.5in}
\centering
\includegraphics[width=2.28in]{P}
\caption{P is a figure.\protect\rule[-2ex]{0.4pt}{5ex}}
\label{figure:p}
\end{minipage}
\hspace{0.21in}
\begin{minipage}[b]{2.5in}
\centering
\includegraphics[width=2.28in]{D}
\caption{D is a figure.}
\label{figure:d}
\end{minipage}
\end{figure*}
\lipsum[2]
\end{document}
resulting in

Assuming nothing extreme is going on in the caption, you might consider adding \strut to the both caption lines. Of course, that wouldn't help in the extreme case I've demoed here.
Essentially I'm suggesting you make sure the heights and depths of your two captions are equal.
\includegraphicsthan you are for theminipage. – A.Ellett Oct 09 '13 at 01:19