First off, this has to be one of the best mods out there right now!
Secondly, I seem to be having some serious issues with both the Common Berthing Mechanism, and the APAS. If I have them connected while in the VAB or SPH they stay connected perfectly and work fine, but when I try to dock, they both behave in the same way. If I try to dock, the ports get attracted to each other, make contact, but refuse to dock/connect properly. I have tried using every combination of passive and active objects just to ensure that it was not my fault, but I don't seem to be the issue.