It only follows that elements with scrollbars in positions other than the top would have a scrollTop of > 0. If you have an element without scrollbars then one would expect that their scrollTop position IS 0 as they have nowhere to scroll to.
 
I'm not exactly sure what the problem is.
 
EDIT: Just in case that it is not explained properly in the jQuery docs:
 
scrollTop() => position of scrollbar for element (window/div/anything scrollable)
 
$("#element").offset().top => position of element relative to page
 
$("#element").offset().top - $(window).scrollTop() => position of element relative to scrolled area.