Michael Kifer writes:
I am almost sure that this is because your cursor is not in the control
buffer. Ediff commands work only out of the ediff control buffer.
Note that if you set up the defaults Enrico cited (or equivalently,
from the menubar select "Tools/Ediff Miscellanea/Use toolbar with
Ediff control buffer" and deselect "use separate frame for Ediff
control buffer") then there is no place to put the cursor so that it
will be in the control buffer! If Ediff is designed so that it cannot
work this way, then it shouldn't be allowed to set up the defaults
from the menubar this way.