Mednafen must not be 100% accurate to real hardware. The second one isn't as bad but it's there.
You said the clipping happened around when Bami says "come at me boy" when Eldeel is talking? There is two ways that scene can go down, 1) when your in Adol's normal form and 2) When your in daemon form.
I got clipping when you go in as 2) (using mednafen) but not in 1).
Joe, I'm assuming you did the part as 2) and Bonknuts did it in 1)?
If that is the case, then can I assume there is only two clips in need of fixing?