Could replenishing occurs if there is a wait order before processing the next order, when you don't have underway replenishment (or have it but you are going too fast) ?
Because right now, if there is an order, any order, even one where you are not moving, then it won't work.
And the issue is that you can't automate: Move to waypoint, wait a few hours (replenishing would occur, you are not moving), resume travel. You must reach the WP, make sure the order list is empty, wait some hours, and plan the end of the travel.