Do you take special steps with the Ediff frame? That's theother problem case I'm seeing with multiple frames and focuson Windows/MacOSX.
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I typically use `ediff-buffers'. In my setup (non-nil `pop-up-frames' etc.),
each of the two buffers is typically in its own frame; those (portrait) frames
are side by side; and the Ediff Control Panel (buffer `Ediff') is a separate
(tiny) frame.
You didn't say what kinds of problems you see.