I'm not sure if this will be of any help, but I made a couple videos that hopefully demonstrate the issues I have with docking around the mun. In the videos I am always having to fight against the phantom forces which makes docking a lot harder. Also over the course of docking, un-docking, and re-docking my periapsis drops by 5000 meters. This was a clean install with only Kerbal Engineer Redux and Docking Port Alignment Indicator mods installed. I used two of the stock ships (Super Heavy Lander) put into orbit around the mun. I have re-created this in vanilla KSP but don't have any video currently.
This video I just undock, no SAS.
http://plays.tv/video/5781f3112e85cb1ca0/ksp-1-1-3-phantom-forces-or-orbital-drift-
This one I fight against the forces and manage to dock again.
http://plays.tv/video/5781f414e6f22ff95d/ksp-1-1-3-docking-with-phantom-forces
Lastly once re-docked and SAS is turned off, the ship undergoes some strange rotational acceleration.
http://plays.tv/video/5781f47eee049ae755/more-phantom-forces
I have been playing since version 0.18 and according to Steam I have played over 1000 hours. To me there is a definite problem here that wasn't always present, but maybe my problem is different from this one and has another cause. I'm open to any suggestions for a fix that anyone has. More or less posting this just to see if this is what others are seeing.
Thanks