A member of my team found a bug in the IvyResolveJob.java which is mainly due to a misunderstanding of the api we suspect.
IJavaProject.isOpen() has misleading Javadoc. It only returns true when a project is not in a collapsed state. This leads IvyDE to skip all collapsed projects when resolving in the workspace.
See the following thread for details: http://dev.eclipse.org/newslists/news.eclipse.tools.jdt/msg22189.html