tmccobb,
The deployment engine was modified from MyEclipse 10 to MyEclipse 2014 but the behavior in terms of deployment remains almost the same as we now have the Deployment Assembly.
Since it is a Maven project, please make sure that in Deployment Assembly of the EAR, project dependencies are added as projects and not as jars from local Maven Repository.
If the modules are still being packaged as archives, please send us all the .* files (.classpath,.settings,.project etc) and the POM.xmls to help us investigate the issue at our end.
Let us know how it works for you.