When a SOA-P 5.2 server is started in JBDS 5.0.2 and 5.0.1 - this exception is raised:

Exception in thread "main" java.lang.NoClassDefFoundError: org/jboss/bootstrap/BaseServerConfig
at org.jboss.bootstrap.AbstractServerImpl.doInit(AbstractServerImpl.java:190)
at org.jboss.bootstrap.AbstractServerImpl.init(AbstractServerImpl.java:173)
at org.jboss.bootstrap.AbstractServerImpl.init(AbstractServerImpl.java:143)
at org.jboss.Main.boot(Main.java:218)
at org.jboss.Main$1.run(Main.java:556)
at java.lang.Thread.run(Thread.java:722)
Caused by: java.lang.ClassNotFoundException: org.jboss.bootstrap.BaseServerConfig
at java.net.URLClassLoader$1.run(URLClassLoader.java:366)
at java.net.URLClassLoader$1.run(URLClassLoader.java:355)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:354)
at java.lang.ClassLoader.loadClass(ClassLoader.java:423)
at java.lang.ClassLoader.loadClass(ClassLoader.java:356)
... 6 more

The root problem from EAP side is that this stacktrace occurs because it is launched with Java 7, same actually happens from command line.
Now, the question is why does Java 7 get selected when the server is setup to run with Java Execution Environment 1.6 - that is the tooling bug here and which Rob made a patch for.
To describe in cases:
1) Thus if the user have only Java 6 configured in Eclipse this issue should not occur.
2) If the user has only Java 7 configured in Eclipse this error is expected
3) If the user has both Java 6 and Java 7 configured and server adapter is configured to use Java 1.6 Execution Environment (which it is by default) then one would expect it to pick Java 6.
Case 1 and 2 works - its case 3 that is failing.