After r231121 the <modules/> in poms were ignored. I tracked the changes, and it was obvious: merge code didn't merge the Modules section, and possibly other sections aswell. Also putting all normal model build info in a profile and then copying profile data back to the model seemed odd to me. Now only data from profiles that actually get merged is merged.
maven/components/trunk/maven-project/src/main/java/org/apache/maven/project/injection/DefaultProfileInjector.java