The settings in the Java Build Path become "unbound" between JBDS restarts. I have seen this on multiple Windows machines (32-bit JVM) and have heard that it happens on Linux as well.
Specifically with the SOA Platform 5/ESB Libraries but sometimes with the JVM/JDK as well.
My Projects are here:
http://anonsvn.jboss.org/repos/labs/labs/jbossesb/workspace/bsutter/soa5demo_eclipse/