In what way does it display on different places, what is your desired behaviour, and can you give a sample page?
Here is how the script itself calculates the top position of the popup (lightbox v2.04, zip download, js/lightbox.js, lines 229ff):
// calculate top and left offset for the lightbox
var arrayPageScroll = document.viewport.getScrollOffsets();
var lightboxTop = arrayPageScroll[1] + (document.viewport.getHeight() / 10);
var lightboxLeft = arrayPageScroll[0];
this.lightbox.setStyle({ top: lightboxTop + 'px', left: lightboxLeft + 'px' }).show();
As the script uses Prototype's document.viewport object, the script positions the popups at 10% inside the current scroll position, like this:
------- page start
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------- scroll position top
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------- start of lightbox popup
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------ scroll position bottom
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------ page end