This was posted by WGTNiblick in another thread on 7/06/2012:
"We will look into the putts being counted against your ball life. If this is happening we will fix it as soon as possible as putts should not affect ball life.
Thanks."
I'm not sure how WGT plans to reimburse people for the golf balls expended in the tourney but they are aware of the problem and have apparently been pouring over the code for a while.