Setting the camera on manual and the setting the flashes on manual do two completely different things. With the flash on manual, it puts out a given amount of light regardless of what the camera does with exposure. If the camera is set on P, and the flash set on manual, the camera will measure the ambient light and provide the exposure for that and ignore what the flash is doing. In all likelihood, that will include a wide open aperture or close to it unless the subject is pretty bright without the flash. The reason the camera ignores the flash when flash is set to manual is that the flash does not prefire its exposure burst, so the camera has nothing to base its exposure on except ambient light. If the camera is on manual, you set the aperture and shutter speed you want and the camera does what you tell it to do.
With an EX flash set on automatic, the camera will measure the light, even if it is set on manual, and tell the flash to quit putting out light when it has put out enough. Most of the time, the camera is right, but sometimes it can't figure it out. In those cases, use flash exposure compensation or set the flash on manual and figure out what exposure to give it. You can adjust the flash output to do this or adjust the camera aperture, but keep the camera on manual or you will have the problem you are having.
So, to sum it up, you have been doing exactly the opposite of what you should be doing.