See .offset() here in the jQuery doc. It gives the position relative to the document, not to the parent. You perhaps have .offset() and .position() confused. If you want the position in the window instead of the position in the document, you can subtract off the .scrollTop() and .scrollLeft() values to account for the scrolled position.
Here's an excerpt from the doc:
The .offset() method allows us to retrieve the current position of an element relative to the document. Contrast this with .position(), which retrieves the current position relative to the offset parent. When positioning a new element on top of an existing one for global manipulation (in particular, for implementing drag-and-drop), .offset() is the more useful.
To combine these:
var offset = $("selector").offset();
var posY = offset.top - $(window).scrollTop();
var posX = offset.left - $(window).scrollLeft();
You can try it here (scroll to see the numbers change): http://jsfiddle.net/jfriend00/hxRPQ/