I encountered the problem while dealing with contents stored under the JCR ametys:plugins root node.
The GetContentInformationAction that is widely used by the CMS to retrieves info about contents manipulated by the user in the CMS workspace evaluates systematically the right context to :

"/contents/" + content.getName();

This may causes conflict while processing the user rights for a given content.
I guess there issue is also valid for subcontent, that are physically stored under a content and hence are not direct children of the JCR content root node.