manstein, at what Gamespeed were you fighting Gaomdo ?
Such a bug was already noticed to appear in the Gaomdo fight (at version 1.7), if playing on Slow or Normal Speed. (Aero tests his Bosses only on High Speed)
According to the BugList on page 1 this Bug was fixed.
I had no problems on my last playthrough, but I didn't reduce the speed for this boss, so my guess is, that the old bug is back...
(So please try to fight him at high Speed and with some luck this solves the problem)
EDIT: I just tested myself. The old Bug still persists. If you fight Gaomdo on Slow or Normal Speed he disappers, during the event when he teleports in Phodom's back and releases some shockwaves!