It seems, all the text boxes are aligned at the top of the page, irrespective of the node position. The attachment is the latex output of a simple tikz flowchart example.
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\documentclass{article}
\usepackage{flowchart}
\usetikzlibrary{shapes,arrows}
\begin{document}
\pagestyle{empty}
% Define block styles
\tikzstyle{decision} = [diamond, draw, fill=blue!20,
text width=4.5em,text badly centered, node distance=3cm, inner sep=0pt]
\tikzstyle{block} = [rectangle, draw, fill=blue!20,
text width=5em,text centered, rounded corners, minimum height=4em]
\tikzstyle{line} = [draw, -latex']
\tikzstyle{cloud} = [draw, ellipse,fill=red!20, node distance=3cm,
text width=3em, minimum height=2em]
\begin{tikzpicture}[node distance = 2cm, auto]
% Place nodes
\node [block] (init) {initialize model};
\node [cloud,left of=init] (expert) {expert};
\node [cloud, right of=init] (system) {system};
\node [block, below of=init] (identify) {identify candidate models};
\node [block, below of=identify] (evaluate) {evaluate candidate models};
\node [block, left of=evaluate, node distance=3cm] (update) {update model};
\node [decision, below of=evaluate] (decide) {is best candidate better?};
\node [block, below of=decide, node distance=3cm] (stop) {stop};
% Draw edges
\path [line] (init) -- (identify);
\path [line] (identify) -- (evaluate);
\path [line] (evaluate) -- (decide);
\path [line] (decide) -| node [near start] {yes} (update);
\path [line] (update) |- (identify);
\path [line] (decide) -- node {no}(stop);
\path [line,dashed] (expert) -- (init);
\path [line,dashed] (system) -- (init);
\path [line,dashed] (system) |- (evaluate);
\end{tikzpicture}
\end{document}
