From the rhq 4.0.1 release notes
If you want to ignore resources, there is sometimes a red box saying "could not ignore.." - this is harmless. If you refresh the auto-discovery portlet, you will see that the resources are indeed ignored.
verified 10/5/2011 by ignoring several resources. did not observe red box.
changing status of VERIFIED BZs for JON 2.4.2 and JON 3.0 to CLOSED/CURRENTRELEASE