JBoss-IDE 1.4 ships with xdoclet 1.2.1 modules installed. This module only supports xdoclet tags up to EJB 2.0.
You need to upgrade the xdoclet jars in your eclipse plugin directory.
Basically get xdoclet-libs-1.2.2 from Xdoclet and unzip/untar the file to a tmp location. Then remove the current xdoclet jars. You basically want to delete $ECLIPSE_HOME/plugins/org.jboss.ide.eclipse.xdoclet.core_1.4.0/xdoclet*. Then copy the unzipped contents of xdoclet-libs into that directory. After changining your xdoclet configuration in the IDE to reflect ejbSpec 2.1 and JBoss 4.0 you should be good to go. If you try to use 2.1 descriptors with JBoss 3.x it won't work.