There are times when the Capital will not return to it's "starting spot" once a country retakes all the zone bases tied to it. Last time I was in Blue (when it was Trinity, last week if I recall), nits had like half of the map in their possession. When I took a look at their Capital, it was still next to the HQ. More than likely a bug, but when a country retakes the zone bases for the Capital, it's suppose to return to it's starting spot. At least that is my understanding about it.