I don't mean to turn this into a necrothread, but I thought I'd give an update. Using MechJeb on both modules doesn't seem to help; they spend more than an hour trying to align, and when they do align and dock, one of the pairs of ports is, again, not docked. I concur with Arbolus and Jason, for when I decoupled the first, properly docked module and then tried to dock the second one, that one docks fine and the first one has problems. So the problem is mirrored and doesn't seem to have to do with the modules themselves. In my next station, the central pillar will probably use the exact same parts as the outer pillars, to completely bypass this alignment issue. But it still bothers me that in the VAB I was able to make them all snap together just fine, and yet they won't dock out in orbit. It would be a great feature to be able to measure out the distance between docks to see if they'll dock correctly. Or to be able to force two nearby ports to snap together, regardless of miniscule alignment problems. Maybe there are addons that can do either of these? I've resolved to discontinue the current project, recover my crew, and deorbit the station. Enjoy the pictures, and thanks to everyone that answered.