Check to see if exposure compensation has accidentally been set to a low, negative number. Or, are you in manual mode with a very high shutter speed and small aperture? Just a couple of ideas.
Long-billed Dowitchers spend all their time either bobbing their head up and down searching for food with their long bill, or preening to keep their feathers in good shape. :)
With a good diffuser, I think flash on macros normally looks quite natural and gives a lot of advantages. I don't have a good flash set up like you do. Wish I did. :)