Trajectories change when warping, and also a 'repulsion' kraken

[IonMage]

I've been having trouble with docking thanks to the fact that vehicles have trajectories that are 'shifted' when I enter either normal warp or physics warp.  I'm docking a particularly huge vehicle to a station, using plasma RCS, so timewarp is pretty much mandatory right now.  I know this problem has been reported with hyperedit, and I think Better Time Warp, both of which I've used before, but uninstalled because of this.  It is still happening though, so it must be something else.  Only guess I can come up with is kopernicus, since its the only one I can think of that does anything with coordinate/positioning values.

 

In a previous time, when I still had this ship docked to this station, just entering time warp would sometimes shift my orbit as well, turning a 490km circular orbit into something along the lines of a 390km/610km, as well.  I suspect this is related.

 

Also, for a while I've had this odd thing where, upon trying to dock a vehicle to another, there would be some kind of 'repulsion kraken' that would 'shove' my ship when it got too close to the target.  As if they were like magnets of the same polarity.  Restarting the game usually resolved this, but since this is now happening in tandem with the above problem, I'm going to take the chance to ask here.