I never had root rot in S/H, two of my Mokaras have its roots touching the bottom of the pot now...and its all large growing like pecils under water...I have 1/4 of the 6 inches glass vase with water
so I dont understand why that is happenning to you.
if you read Ray's instructions to the letter, then you have the correct S/H method
do you have an electric heat pad to help the roots?
its winter and cold roots under water will sure rot it