I know this thread is a couple months old, but thought I would let everyone know... I too was getting errors about Emacs not being installed (even though it was, in fact, installed) with the stable CiaoDE 1.14.2 release.
I downloaded the latest development version, CiaoDE 1.15-1712-ga8c821b, and it installed and downloaded/installed Emacs and both are working for Prolog (though not the Java integration.)
This is on a 64bit Windows 7 PC.