Thanks for the replies, but they don't even engage when they actually touch, without an angle (I put some better pics up). Tried to disassemble the station, dock with a small (5ton) module first, but it still didn't budge. I'll do some tests to see if it's a problem with the design (I think I read somewhere that clipping issues can make the ports not think they're on top of the rocket), but if it persists, I might deorbit the lot and assemble a new station already in position.