As in title, when I apply stroke value to a path created with pen tool in Ai CS 5.5, this path is being moved. That doesn't apply to all shapes I made. Is there a setting that needs changing or what. I'm unable to create a proper, precise drawing because of that.
I hope I'm understanding your question correctly. It seems you may want to tweak the stroke alignment option a bit. Namely align "stroke to center," "stroke to inside" and "stroke to outside." If you do center align, then you may not notice the shift.
Edit: I understand your problem now.
You need to disable "Align to Pixel Grid" in the transform option panel for this path.
Ahah! I've figured it out!
I noticed that it only started moving it when going from certain values - so for example from 2px to 1px. So I then had a 1px line and was trying to align it to the centre but it wouldn't... so I realised it must be snapping to the pixel grid. So if you turn off "Snap to Pixel Grid" in the transformation window then the path does not adjust itself to lock to the pixel grid! Ahhh that was REALLY bugging me!