Since the last few builds, the docking AP starts moving away from the target indefinitely.
Even when lined up perfectly. I saved and replaced current production version and the docking works. Probably some bug with safedistance.

I've tested several builds and I can confirm that this bug started with build 170, so probably commit 44cba06

I can confirm this one. I'm presently running build 169 to get around it. It seems related to where the software locates the "starting point" when you're trying to dock large vessels. I've seen the safe distance and target size numbers up over 200, so that puts the starting point outside the range that you can select a docking port as a target. You back out to try to get to the starting point and before you get there the target docking port is cleared.

I talked about this on the forums at post 5642, but no one said anything there.
http://forum.kerbalspaceprogram.com/threads/12384-PART-0-23-Anatid-Robotics-MuMech-MechJeb-Autopilot-v2-1-1?p=1047532&viewfull=1#post1047532

closing as both an old bug and in favor of #1059