Eclipse Neon Debug mode is not working - eclipse

I was using Juno and debug mode is working fine in that. But in Neon as shown in attached, is not detecting the debug mode.
I have made several attempts as below.
I'm Sure I'm running on Debug mode
Break points are not skipped
Clean the project and executed again
Restarted the eclipse and machine
Executed the code with a comment in console, for making sure the code line is executing.
-- What else I can try to make this working
UPDATE
I'm getting error as
(https://bugs.eclipse.org/bugs/show_bug.cgi?id=468908)

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