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The ST400 is new, then, if I understand correctly.
You've made a compass swing, and find some difficulty in calibrating degrees with compass readings... do you have your autocompass hooked up in the system also? check its connection, and its function, if possible.
On some boats, of course, a magnetic compass has different degrees of deviations (from true north) at different points of the compass, owing to large metal masses being aboard (e.g. the boat's engine, etc.) Could that be the problem, simply? What degree of variation are you seeing?