say you have a project/out directory for your compiled classes. The top level package should be something like com. So create another subdirectory of out called META-INF. In the META-INF directory place you ejb-jar.xml file. Then from out build your jar.
jar cfv myProject.jar *.*
That should capture all the contents of the out directory and it's subdirectories and place it in the myProject.jar file. Since META-INF is defined as a subdirectory, it will use that directory for the manifest in the jar, rather than creating a Meta-Inf directory. At least, that's how I do it and I haven't had the problem you describe.
Hope that helps.