When connecting two objects with a line 99% of the time I want the line stuck on the magnet I choose, not jumping to the closest magnet as I move the object. Visually all magnets on a object are not all the same.
How do I set omnigraffle to respect my connections?
In OmniGraffle, it makes a difference whether you’re connecting the line to an object’s center, or an existing magnet on that shape. Given the behavior you’ve described, it sounds like your lines are connected to the overall shape, rather than a particular magnet on that shape.
If you click in the middle of an object when connecting a line (the shape will glow with a highlight), then the line is considered attached to that shape’s center. When you subsequently move that shape on your canvas, the line will snap to the closest magnet on that shape.
In contrast, when drawing your line if you attach it directly to the magnet (in which case the magnet will glow with a highlight), OmniGraffle will remember that you’ve attached to this particular magnet. The line will remain connected to this magnet when subsequently moving the shape on your canvas in this scenario.