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.
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