Well at f/2.8 more light will be let in, but at the expense of depth of field. In everyday situations (portraits, sports etc) the bigger aperture (smaller f-number) is great, as it can separate the subject from the background. At macro levels though, f/2.8 gives such a small depth of field that you'll be hard pressed to get the whole of the subject in focus.
Reducing the aperture to something like f/11 will increase the amount of your subject that's in focus, but reduce the amount of light hitting the sensor. For this reason, to get properly exposed, and well-focused macro shots, a flash is pretty important, or it'll be under-exposed. If you take a few more shots demonstrating the problem then someone will be able to confirm if this is the case!
Chris
Edit: Again, sorry if I'm speaking down to you, I've only just started understanding all of these things and I'm just writing down my thought process!