A little more info after working on this tonight:
I turned off my water supply and emptied the water lines so no more water ran into the toilet when I pushed the lever. I then cleaned it all and wiped it out. At this point I pushed the lever again just to get any remaining drops out and noticed that after the flap closed and no fresh water ran into the bowl, it started filling (at the seal only, the bowl was dry otherwise) with foul smelling cloudy water.
How is this possible? Is it the seal? My black water tank is not full, I can see down in there when the flap is open. Where is the foul water coming from?