I think that only one planet in a system will allow you to repair habitat at one time - they all display that they can, but only one works.
I built three colonies in the one system and then increased the size of each to the point where they were large enough to repair habitat. The first one large enough worked as expected. The second one did not work, but I thought it may have something to do with the fact that it had two planets nearby with overlapping gravity wells, so I started trying to see if I could find a place where it did work. When the third colony became large enough to repair habitat, it worked but now neither of the first two work any more.
The order in which they worked leads me to believe that the planet with the highest number (furtherest from the sun) is the one that works.
DancingFool
