(Note: ediff-setup-windows-plain sets up ediff to use a 3rd window for the controls instead of opening a new floating frame which is what I prefer.)
Now, when I invoke ediff from emacs I get a nice 3 window ediff session in one frame (without a toolbar). Exactly what I want.
But if I invoke ediff from the command line like this...
emacs --eval='(ediff-files "/tmp/x" "/tmp/y")'
... the control window is gone!
Now here's the crazy part: If I get rid of the (tool-bar-mode nil) line in my .emacs OR if on the command line I add the command (tool-bar-mode t) I get the 3rd window back, but I also have a tool bar (which I don't want).
Can anyone try this and tell me if you can reproduce this problem on your setup?