Following jars differ shipped in the EAP and Seam:

seam/lib/activation.jar
seam/lib/gen/bsh.jar
seam/lib/commons-logging.jar
seam/lib/javassist.jar
seam/lib/jbosscache-core.jar
seam/lib/slf4j-api.jar
seam/lib/gen/slf4j-api.jar
seam/lib/concurrent.jar
seam/lib/ejb3-persistence.jar
seam/lib/hsqldb.jar
seam/lib/jaxb-api.jar
seam/lib/jboss-common-core.jar
seam/lib/jboss-deployers-client-spi.jar
seam/lib/jboss-deployers-core-spi.jar
seam/lib/jboss-jmx.jar
seam/bootstrap/deploy/jboss-local-jdbc.rar
seam/lib/jboss-logging-spi.jar
seam/lib/jboss-system.jar
seam/bootstrap/deploy/jboss-xa-jdbc.rar
seam/lib/jcommon.jar
seam/lib/jfreechart.jar
seam/bootstrap/deploy/jms-ra.rar
seam/lib/jsf-api.jar
seam/lib/jsf-impl.jar
seam/extras/mail-ra.rar
seam/lib/quartz.jar
seam/lib/stax-api.jar
seam/lib/xercesImpl.jar

Hey Marek,
if you know what's wrong, then fine, however if you need diffs for all these jars, just let me know, I'll try to come up with more meaningful information.