All I can offer is my .emacs file:

(defun my-jde-mode-hook ()
  ;; Java mode sets its style before running c-mode-common-hook, so
  ;; the java style is clobbered with the bsd style set above. This
  ;; resets the style to Java.
  (c-set-style "java")
  )
(add-hook 'jde-mode-hook 'my-jde-mode-hook)

Notice the differences in definitions:

You: (c-set-style "my-java" my-c-style t)
Me: (c-set-style "java")

I'm running Emacs 20.3.1

Noel

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