Goddamnit. Forgot that Master codes are also abbreviated as (M).

Ok. NOW  issue 6367 : https://code.google.com/p/dolphin-emu/issues/detail?id=6367 is fixed.

I wish I'd remember these things before committing and not after.

Data/User/GameConfig/GOME01.ini

@@ -5,8 +5,6 @@ EmulationStateId = 4
 EmulationIssues = Bad Graphics
 [OnFrame] Add memory patches to be applied every frame here.
 [ActionReplay] Add action replay cheats here.
-$(M)
-C4091E74 0000FF01
 $Score Once To Win Game
 00537C69 00000003
 0053932A 00000003