error on jboss runtime in eclipse after patching jboss eap 6.2.2

We patched to eap 6.2.2 because of this bug https://bugzilla.redhat.com/show_bug.cgi?id=988280 . It seemes to be ok with getops but now we have troubles to build with eclipse (kepler with jboss tools 2.4.1).

We got invalid jar files for the server modules.

Example :

Archive for required library: '/home/jboss/jboss-eap-6.2/modules/system/layers/base/javax/el/api/main/jboss-el-api_2.2_spec-1.0.2.Final-redhat-1.jar' in project 'VigilanceServeur' cannot be read or is not a valid ZIP