So I tied to evoke error reporting dialog with the following scenario:

1. import Java EE Web Project from central
2. right click in Project Explorer -> refactor -> rename
3. change name, hit OK which will result in errors from org.hibernate stuff

In case of JBDS no error reporting dialog is shown, works in JBT

I also tried org.eclipse stuff:
1. open Properties view
2. create JPA Project (File -> New -> Other... JPA Project)
3. open persistence.xml which will result in NPE from org.eclipse stuff

And again in no error reporting dialog in case of JBDS but works in JBT