It will be clear from .classpath file, if jar is registered as an external resource or workspace resource. Could you please attach your .classpath to https://issues.jboss.org/browse/JBIDE-11386
By the way, looking for quick workaround for you, is it necessary to declare Veto annotation as a qualifier? Might it not work if you add to TransactionPhaseListener some new custom qualifier? By default, bean TransactionPhaseListener has Default qualifier, and adding any other qualifier should strip off Default qualifier from the bean so that it will not be injected.