I am running FindBugs from an Ant task. I have a .fbprefs settings file that I want to use FindBugs, so the error report generated by Ant is the same as the file created by Eclipse.
Unfortunately, the ant task is based on filter files, see http://findbugs.sourceforge.net/manual/filter.html
You should start using filter files, not the Eclipse plugin configuration. Check out this resource: http://docs.codehaus.org/display/SONAR/Project+settings#Projectsettings-Excluderesources
It should help you create a filter that matches the configuration of the Eclipse FindBugs plugin.