Great! Thanks a lot, everything works fine now! Another thing that I noticed is that I can't actually dock to my ISS, since every time when I get close enough it gets teleported 10KM away from me. Not sure if this is actually a bug or I need to adjust some settings on the server.
UPD: ok, I figured it out, if you time warp during docking the server will update the positions and teleport vessels from each other. So one shouldn't use time warp after he's close enough to not use it.
UPD 2: friend just had a weird problem, he EVA'd out of a spaceship and got teleported far away from his ship, no warp was used. Maybe it worth noticing, that for some reason all the ships on the map are blinking for him and if he sets somethings as a target he loses the target fro a couple of seconds every once and awhile.
UPD 3: new glitch, probably related, spaceships get randomly teleported all the time, my ISS is now orbiting the sun (second time this happened) even though it is supposed to be on the orbit of Kerbin. Doesn't seem to happen with landed ships.