Answer: This is certainly a stumper. It sounds like damping off, a fungal disease that attacks a plant right at the soil line. The disease is soil-borne, and can be carried through year after year in unsterile potting soil. The only thing I can figure out is that you are not using clean pots. You said that you are using clean potting soil, but how about sterilizing your pots or flats with a mild bleach solution before filling them with soil? Everything else you are doing sounds just right. So, try cleaning your pots and see if that clears it up. Good luck!
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