I still find this bug very confusing. Projects do not often change from single root to non-single root. if the project is singleroot, it will return those modules at all times, after a clean publish and after a restart. It will not publish them once, then ignore them the next.
Because of this I am very curious what the root cause is. it's very hard for me to imagine when looking throught he code. Have you tried using our GA? There was this bug below which applied to a web project inside an ear project back in CR2. It's possible this issue is related to that, though this time occurring on the web project and it's child libs.
This seems very very familiar to https://jira.jboss.org/jira/browse/JBIDE-6024