Kerbal Space Program

I have set up an asteroid intercept 13d out on an elliptic orbit.I place a maneuver node in the apoapsis and time warp to it in maneuver mode, the orbit changes drastically and the maneuver node ends up shifted close to the periapsis (and the intercept isn't feasible anymore). So I reload a safe and try time warping in the tracking station instead. I warp to where I want to start bruning, leave warp mode and select "fly" for the vessel. But in the vessels map mode I find it is back where I started warping in the tracking station.