Hi sierra,
Ok. If I have the picture correct, the first problem I can see is that you are effectively using the underground (wet) section of the piping as a sediment trap. The section that goes up and over and into the leaf trap has created a slow area for the water to drop its particles trapping all of the debris that can rot and allowing it to settle at the bottom of the riser pipe and cause the smell that you have. It then contaminates the next rain collection as it passes through the pipe. You need to create a sediment trap before the collected water is admitted into the system.
It would also be good if you can create a drain pipe from the lowest level of that underground section so that it can be drained between rain events.
The second thing is that you are putting the fresh water into the top of the tank, but I am assuming that you are drawing you water from the bottom of the tank? The water will stratify, leaving the stagnant water in the bottom with the bacteria that has been carried into the tank.. This needs to be sorted as well. There is more than one way to do this. I can elaborate if you wish.
I can also refer you to a sediment trap design made only of down piping and fittings that is simple to make if you would like.
