I don't have the Prepare ChangeLog item in Project menu. I noticed that I'm able to invoke the function using the key combination Ctrl+Alt+P. I don't have the ChangeLog Entry item in Edit menu either. I have Eclipse Juno 20120614-1722 and ChangeLog plugin 220.127.116.11209211606.
I have discovered the cause of the problem and have posted a patch to both our master repository and the one used for our updates-nightly-juno repo. Please test it out. The patch will be part of Linux Tools Juno SR2.