From a blog (http://karoshiethos.com/2010/01/11/fdteclipse-ant-configuration-same-jre-as-workspace/
I've been looking for a way to force "Same JRE as Workspace" as the default in my ANT build targets under FDT / Eclipse. I haven't figured it out yet, but I finally found where this setting is stored:
Remove the entries for org.eclipse.jdt.launching.JRE_CONTAINER & org.eclipse.jdt.launching.MAIN_TYPE, and Eclipse should use the workspace's JRE.
I'm sure someone could take this information and throw together a plugin / fix? The powerflasher team would honestly make the best candidates.