The easiest explanation for the asymmetric organization of Gustav is that the western half of the storm is over the loop current, while the eastern half mostly is not. Meteorological explanations rarely turn out to be so simple, though, so there are probably some other issues involved. Gustav's inner core has been disorganized since leaving Cuba, as indicated by its elliptical shape and ill-defined presentation on satellite.

Gustav is not a healthy looking tropical cyclone at the moment. The clear area that is occasionally showing up on satellite is not really an eye... it is very close to the center, but it more indicative of a lack of convection in the eastern half of the eyewall. The last couple of IR images show what looks like a ring of intense convection surrounding a slightly clearer area well to the SE of the clear area mentioned above. Do not be fooled, that is not where the center of the storm is. Looking at a satellite loop will make that clear, though looking at a static image may give the wrong impression.