Mugen
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after the most recent update, it doesn't support mugen anymore. but before, no problem.
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In general FBX will record any application that uses DirectX or OpenGL. Presumably, your MUGEN build used GDI or DirectDraw for rendering which is not supported by FBX. It might have worked by pure chance, but this behaviour is not guarranteed.
However, we are working on new 'Fullscreen Record' mode which would capture any video output regardless of DX or OGL. This will fix your problem, stay alert, we'll make it public in near future.