Are you running pump gas or non ethanol gas?

If you are running fuel with ethanol, a certain amount of water will go into solution with the ethanol in the fuel before it hits a phase separation point, at which the ethanol becomes saturated and the EtOH and H20 fall out together and go to the bottom of the tank.

You can actually measure the ethanol levels in fuel utilizing water. That would explain why you have no issues until it hits a certain point.