That is really too bad. I hope that Kubota will fix under warranty as you have noted the issue in the past when the unit is under warranty. These types of issues are my worst nightmare. They linger for a long time and in the end they affect the longevity of the tractor. The only silver lining in this for others with the same symptoms is now they have reason to bring their units to the dealer and have the HST replaced, hopefully under warranty.
I once had a Honda Accord V6 with transmission troubles. The Honda people kept saying, "We have never seen one of these transmissions fail" Famous last words. It was the torque converter and one day it just locked up for good.
Good luck and keep us posted.