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/GUNE5D.ini

@@ -7,9 +7,6 @@ EmulationStateId = 5
 EmulationIssues = 
 [OnFrame]
 [ActionReplay]
-$(m)
-0020016E 88000000
-C40FE518 00000800
 $Player 1 health 9999
 0020004A 08000000
 04277374 461C3C00