Could you list some more details about what you're using? What version of Eclipse? Is this in the WebSphere Development Tools plugin, or, is this Rational Application Developer?
There is a chance you may have security enabled on the WAS instance, and not configured in the server configuration in RAD/Eclipse. Make sure you can log in via a browser to the WebSphere Integrated Solutions Console first (i.e. https://localhost:9043/ibm/console). If those credentials work, be sure to plug those into the server config in your RAD/Eclipse IDE.
Kenny Smith
Principal Consultant
IBM Champion
www.strongback.us