First, I assume that the "header tank" is part of the closed system (it has a pressure cap)?
Second question for you involves your method of determining the system capacity.

The thought that comes to my mind is that you have an air pocket of some kind somewhere. We run into this with certain automobiles (Porsche Boxter is famous for being difficult to re fill) where lines run low between different components in the system. The answer there is to use a vacuum fill system. The behavior of your system sounds exactly like the first time I ever tried filling a Baxter without the tool....

Curious,
Bruce