There are many ways you can organize and deploy WebObject JavaClient applications. One of the ways to do it is through WebStart. You could manually create a WebStart app, but WebObjects can also do it for you, taking care of JNLP creation, jar organization, and many WebStart nasty bits.
There is a problem however. The WOLips incremental builder will not automatically create the required jar of your client-side classes and place it in the project.woa/Contents/WebServerResources/Java/ directory as is required by a WebObjects WebStart Java Client application.
Without the client classes placed in WebServerResources, Eclipse's built-in Run... command will not work properly as the client application will not have access to its classes and WebObjects will silently fall-back to EOGenericRecord. This causes the confusing condition of the application launching and likely not generating any errors, but not working correctly either.