I've bound the mouse-3 to a custom function, with a statement
(define-key org-mode-map [mouse-3] 'foobar)
But when I revert some .org file, the keybinding of the mouse-3 goes back to the default and it displays the context menu.
I have this problem every time I start up emacs too. The init file loads, but the mouse-3 won't run the custom function I assigned for the org-mode in org-mode buffers. And when I eval-buffer the init file, it gets fixed until I revert those buffers.