If i remember correctly, the Seam Plugin is said to work under Netbeans 5.5 with Seam 1.2.1 GA which works on JBoss 4.0.5 (JEMS Installer with ejb3 profile).
I think you are using incompatible versions. With JBoss 4.2, they threw out Myfaces to put the Sun reference implementation in there instead. Re-adding the jar files in the lib folder wont be enough, I think.
So, basically, figure out the correct versions and consider not using Netbeans 6 right now. I have used the latest build today and it threw exceptions while editing a regular facelet file. That IDE is awesome, but not production ready let alone near a beta status.
Thanks for the reply. I also thought the same and now have switched to myeclipse. Let me see if i face any problem with it.