I float over the Userbase and I appear to dock, I even seem to buy a commod but when I undock from the base I'm 7k north of it. I suicide and do the whole thing over again but when I undock I'm now 4.5k south now only this time I notice the staised ship is in the path of the planet with the large orbit so I wait until it comes around again. I see the planet and get in my ship and it promptly transports me another 1k away from said planet. I have waisted money and time on this so fix it please.

This is probably related to the fact that I've noticed that when you dock while moving, the game doesn't appear to update your position according to the movement of the base but rather according to what you were doing before. If you have your radar up, you'll notice it doesn't stay centered on where you are. Below is a fantastic example. Notice the distance to the object i have selected on my radar screen.

Another issue that is probably related is that sometimes when you remotely toss something from one of your docked ships, the debris sometimes appears not on top of the AI base but some arbitrary distance away. (seen over 1k before)

The reason this is so apparent when dealing with emp bio is that your client and server don't talk as much when you don't have an engine equipped (or so my theory goes...) so the disparity grows much more apparent.

A third thing that may or may not be related is a desync issue I noticed that sometimes the client arbitrarily rotates planets suddenly. Here's what just happened to me: I tried docking at my moving base on a planet, it said "Docking denied: Too far away". So I warped out of my galaxy and flew quickly back over to it and was about to dock when the whole planet abruptly shifted about 140 degrees... I was able to dock where the base used to be, but not where the client now displayed it.