I'm not sure what the difference is between lombok and lombok-maven-plugin, but my projects are configured with this dependency:
org.projectlomboklombok-maven-plugin1.16.12.0
I haven't experimented with root and submodule poms yet, as my projects all tend to be rather isolated from each other. Not sure if that could be causing an issue for you.
If you are using Eclipse, have you run the lombok.jar file and pointed it to your eclipse.exe file? it needs to modify the .exe in order for Eclipse to know that those getters and setters are coming, so that Eclipse doesn't complain during development.