Open up FF3usME, scroll down to Enkidu, enter the AI. If there is an FC 12 00 00, add this after that line:
FB 06 30 (there's a chance Gilgamesh is monster 2 instead of one, if this still doesn't work try FB 06 31).
If there is no FC 12 00 00 line, add it after the first FF.
That should do it.
Also, since you're using Snes9x, why not use the Record AVI feature it has?