What you said sounds similar to what's happening to me. I did not know this was an issue :/
EDIT: You're right, my camera's doing exactly the same thing. The flash goes off and then the shutter takes the picture so I get a dark picture
Reset my settings and it gave a brighter picture as everything was in sync. In the earlier photos it did actually go off during the photo, but gave a darker photo (maybe it fired a second too early)