Shimano Alfine lever does not seem to pump oil into the hose even with reservoir full
It turns out I just needed more patience. To fill the brake line, you need to:


Make sure reservoir is full of oil. 
Open the bleeder port
Squeeze the lever in
Close the bleeder port
Release the lever 
Wait about 10 mins for the oil to s.l.o.w.l.y. get sucked down into the line. 
Repeat until oil is coming out of the port. 


There must be a very small bypass port inside the lever assembly to let the pressure equalize over minutes.