What's on path_to_flex_web_app/WEB-INF/classes/flexPmd folder? Theoretically the plugin shouldn't writte anything to any project / file in your project. Can you provide some further details on what you have there ?
I performed a "clean" operation on the Tomcat server instance and the problem just went away. It's being doing fine since that. I'll let you know if I see this issue again.