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The docs for .position() clearly state that they return the "current position of an element relative to the offset parent." - explicitly not the position based on the viewport. However, .position does report different results based on where it is moved on the page due to scrolling.
Here's a fiddle: http://jsfiddle.net/6g5upsvq/ Click the button, then scroll and click it again. The .offsetTop direct from the DOM stays constant, but .position changes.