partly fix #2656, I guess. This was a shortcoming in the architecture that allowed the joypad API developers to make a mistake. There will be other fallout from that, but this is the minimal fix.

src/BizHawk.Client.Common/Api/Classes/JoypadApi.cs

@@ -68,6 +68,18 @@ namespace BizHawk.Client.Common
 				var buttonToSet = controller == null ? button : $"P{controller} {button}";
 				if (state == null) _inputManager.ButtonOverrideAdapter.UnSet(buttonToSet);
 				else _inputManager.ButtonOverrideAdapter.SetButton(buttonToSet, state.Value);
+				
+				//"Overrides" is a gross line of code in that flushes overrides into the current controller. 
+				//That's not really the way it was meant to work which was that it should pull all its values through the filters before ever using them. 
+				//Of course the code that does that is in the main loop and the lua API wouldnt know how to do it. 
+				//I regret the whole hotkey filter chain OOP soup approach. Anyway, the code that 
+
+				//in a crude, CRUDE, *CRUDE* approximation of what the main loop does, we need to pull the physical input again before it's freshly overridded
+				//but really, everything the main loop does needs to be done here again.
+				//I'm not doing that now.
+				_inputManager.ActiveController.LatchFromPhysical(_inputManager.ControllerInputCoalescer);
+
+				//and here's where the overrides managed by this API are pushed in
 				_inputManager.ActiveController.Overrides(_inputManager.ButtonOverrideAdapter);
 			}
 			catch