I can’t rperoduce this. I installed Eclipse 3.2RC5 and MyEclipse 5.0M1 clean install, configured them with JBoss 4.0.2 and deployed a test project with an exploded deployment (make sure you are using exploded). As I made changes to the JSP and saved it and went back to my browser to refresh, I saw the changes. I also checked the deployment tool and the project was not out of date.
Are you running a script to update any files in your project? That *will* cause out of date warnings.