After creating a project archive from the Project Archives window, consisting of a war file, a jar file and EarContent folder it creates the ear successfully.
After restarting eclipse (or closing and opening the project) the Project Archive does not load the jar and war archives, only the EarContent fileset.

Testing a little further, adding only a jar archive and a fileset works, but when adding the second jar (war in this case), the project archives loads only the fileset, discarding both jars.