It seems that by default the FDT/ANT task to launch a browser, (fdt.viewDocument location="file") triggers the browser in the internal SWFbrowser. What I wanted was my system browser. The ANT exec tags provides you the option to do just that. It allows you trigger the browser of your choice. The full ANT script is:

[project default="doMyProject" name="PeugeotConfigurator"]
[property name="scr.dir" value="${basedir}/src" /]
[property name="deploy.dir" value="${basedir}/bin-debug" /]
[property name="browser" value="firefox" /]

[target name="doMyProject"]
[fdt.launch.application projectname="PeugeotConfiguratorMainStateMachine_FDT4"
mainclass="${scr.dir}/PeugeotConfigurator.mxml" target="${deploy.dir}/PeugeotConfigurator.swf" /]
[exec executable="${browser}" spawn="yes"]
[arg line="${deploy.dir}/index.html"]
[/arg]
[/exec]
[/target]
[/project]

Please note this is tested on Linux (Ubuntu). I have no idea if it solves the problem on Windows. Please use > and < in place of ] and [.