The puffer fish was deep in a hole, was unable to light up with both strobes, hence the shadow. I'd post the photo but a little confused, does wetpixel host the jpg or do I have to link to it from another site?
Problems solved as far as the strobes go, Canon seems to have a problem, just best to avoid aperture preferred.
You've gotten some good explanations of why the strobes aren't providing enough light. The settings you're using are adequate for ambient light. There's enough light for exposure without much flash so the camera shuts the strobes down early. Take the camera out of program mode or aperture or shutter speed priority and use manual mode to control both shutter speed and aperture.