I have seen some posting around regarding the error publishing failed in RSA or RAD.Then u open server perspective save it and then again u get the same error.(

If you continue getting this try this out.This helped me.

Remove all the ears added to your server.Then open the server perspective and click on the Applications Tab.See if some application is still shown there.
If it is there try this.
go to command prompt and change to AppServer/bin.
(Say C:\WebSphere\Portal5UTE\ApplicationServer)
Start server1 and delete the ear using WAS_AdminConsole. Start WebSphere _Portal from bin of Portal_root also .It should start WebSphere_Portal .
Log into Portal. GO to Admin console and delete the web module from webmodules and from applications.

Stop both the servers again from command prompt.

Try to start server from RSA.THis worked for me.Good Luck!