I just came across this topic and since it looks like you didn’t get a response I'll take a stab at it.
I'm not familiar with that game but I do use OpenEmu (I love me some Legend of Zelda game boy games), and it does allow outside keystrokes in the macros I've built for it.
A couple of observations:
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Your keystroke commands in your OpenEmu macro aren't being sent directly to it like your DeSmuME macro... did you try configuring them that way to see if OpenEmu would respond to them?
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your pixel coordinates are absolute coordinates, which means the app window must be positioned in the exact same spot every single time. Even a slight movement of that window would likely cause the pixel condition to return false. So you might double check that your emulator window size and position stays the same BEFORE running that part of the macro, perhaps by using a manipulate a window action to ensure the following action looks in the right spot.
Just spitballing here...maybe you've already figured it out already since this was quite a few months ago.
-Chris