...We deal with this all the time with modern autos. It can be really challenging to get all of the air bubbles out and the results are exactly what you are describing....
If you do not get it working easily, you might try eliminating one or both of the external loops and retesting the system without the possibility of a loop to confirm that all is well, then you might try one loop at a time to see which one (or the combination of both) leads to the issue. Does not sound like much fun....
Something like this might help... http://www.autobodytoolmart.com/uview-airlift-coolant-filling-tool-550000-p-13770.aspx

Good luck!
Bruce