Like Rusty says, running it with the cap off, lets the air pocket bubble out of the highest point.
If the cap is on, it keeps pressure on the system and the releasing of trapped air is not as easy.
When the cap is on all the way, the water has to build pressure to overcome the spring in the cap, as the hydro pressure builds, its pushing and absorbed into the air pockets and delays the opening of the spring in the cap.
Normally, without air in the system the psi would overcome the spring in the cap and allow the water to trickle into the neck and drain into the reservoir, and eventually exhaust the air.
