Eclipse supports more than one way of referencing libraries, for example MyEclipse hibernate support adds related jars in a separate item which is not in referenced libraries. You see another item in the package explorer under your project.
The result? Almost always, Google Web Toolkit refuses to load these libraries. Apparently the best thing to do is to create a local folder like libs or something, copy the jars into it, and add them from the build path configuration. Otherwise, running the deployed code becomes a nightmare.
There is a really, really thin line between flexibility and complexity, but that’s the one to watch for.