Just a suggestion for using those clear cups. Either tape up the outer cup or use a red one for the outer cup. The light penetration allows algea to grow in the soil and around the roots on the bottom of the cup. I experienced this first hand after going the double clear cup route so I could monitor the water content in the soil because I had some problems with over watering last year. I agree that the burnt roots are from excess water sitting in the cup for too long. You may have to cut back on the amount of water you give them at one time, but water more frequently if needed. You will still need to top water from time to time in order to supply water to the roots in the top half of the cup, instead of trying to water everything from the bottom. That should eliminate the soggy soil in the bottom.