It seems that the borders of the figures itself are not correct. An easy way to check this is to surround each one with a \fbox, e.g. replacing \includegraphics[scale=0.4]{Fig1} with \fbox{\includegraphics[scale=0.4]{Fig1}}.
(Something different: I recommend using \centering instead of \begin{center}...\end{center} because the latter one will produce unwanted vertical space between figure contents and caption.)
You are using the now obsolete package subfigure; you should use subcaption instead.
The reason why the numbering for the subfigures does not reset is because you are not using a caption for the figures (and the subfigure counter resets every time the figure counter is incremented, which wont happen without a caption). A quick fix would be to add
\setcounter{subfigure}{0}
just before each new group of figures to manually restart the counter (or to add
in the preamble
\renewcommand\thesubfigure{}
to suppress the numbering for the subfigures, as you also propose in your question).
An automatic solution can be obtained by using a \caption for the figures; if you want to suppress the name Figure and the label separator : that the use of \caption causes, then one possibility is to use in the preamble
\usepackage{caption}
\DeclareCaptionStyle{mystyle}{name=none}
\captionsetup[figure]{style=mystyle}
\usepackage{floatflt,subfigure}
and to write \caption{} inside each figure environment.
Best Answer
The
subfigurepackage is deprecated; you should use either thesubfigor thesubcaptionpackage.Here's a solution based on the capabilities of the
subcaptionpackage. Eachsubfigureenvironment is assigned a width of0.3\textwidthto have some whitespace between adjacent subfigures.