I'd also like to confirm I'm having this issue. I've reinstalled all parts (including Toadicus' ModuleManager) and I've been testing with a ship that starts with a docked clamp-o-tron port, decoupled, rotated to the other side of the ship, where I have the largest Universal Docking Port, and it simple will not connect no matter what I do. I can make a video tonight showing this action if it helps at all? Simple put there seems to be no magnetism present with the Universal ports. Interestingly enough, when I use the VAB and make a large universal docking port connected to another at the bottom of a ship, and undock them on the launchpad, then drop the landing gear and allow them to sit on top of each other for a few seconds, it will eventually dock after some glitching about as they rub together, but again there doesn't seem to be any magnetism present. I might try this in orbit later today too.
