If you have heavy clay soil, no matter what you put in the run to raise the level, the clay underneath it will act like a bowl to hold the water. The water will sit in the clay basin, even though there is sand or shavings on top. Kind of like if you have a bowl full of water. You can add marbles to the water, but the water will still be there, even if you fill the bowl up with marbles. There needs to be some drainage from the BOTTOM of the bowl, which needs to drain DOWN HILL from the run in order to solve the problem. Until you solve your drainage problem, the standing/stagnant water will continue to haunt you.