Nirth: It's called auto-pilot for a reason. Unless it's an enemy ship or a black hole, I don't think it should be crashing.
I spent quite a few hours in there (mainly X3 Reunion), something like 100+, and I never had those problems. The AP reacting strange yes. moving up and down and similar yes, but it was than me making the mistake of a bad landing vector, like trying to land from the opposite direction ;)
I can't remember the name or setting, but you can also instant dock....So no landing sequence....Yes plain vanilla and the official package, so not modified.
As Bigs mentioned, trying to land or anything with Sinza is bound too fail ;) Especially with M1 or M2 ;)
ahhh and the max. speed of your ship can sometimes cause problems as well. The nice M5 are bound for problems....too quick...I only say Blitz ;)