Unfortunately, the JPA java completion proposals extension point is incorrectly forcing o.e.jpt.jpa.core plug-in activation. Once our plug-in is activated we start listening for java events and facet events, whether JPA faceted or not. In Juno these background threads were converted to the Eclipse Jobs framework. In Helios you would not have seen them in the Progress View, but the same problem existed.
Thanks for entering a bug against Dali https://bugs.eclipse.org/bugs/show_bug.cgi?id=386171 for this problem.
Update: The bug has been fixed for Juno SR1, thanks to JDT Text for their quick turn around on this Dali bug!
Update 2: This problem is still occurring for other use cases. In Juno SR2 there are 3 bugs being worked on that will help resolve this issue. Some of these have further fixes that will need to go in Kepler. See bugs:
https://bugs.eclipse.org/bugs/show_bug.cgi?id=397778
https://bugs.eclipse.org/bugs/show_bug.cgi?id=397606
https://bugs.eclipse.org/bugs/show_bug.cgi?id=386393