I have resorted to using the jetty server adapter for eclipse-wtp. It is working. It should be noted that I am using the vanillla tomcat 6.0.20 from apache to produce the errors listed. It appears to be something related to the roo namespace declaration in the main template. I don't know why that would not be working but it is definitely reproducable with tomcat in eclipse.
Stefan/Ben is there anything I can send you to help you see what I am seeing?