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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Code, edit and compile here:
\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}