I was having the exact same problem. The way I fixed this is by adding
document.viewport.getScrollOffsets()[1] to the
withinIncludingScrolloffsets function in the prototypejs library.

  withinIncludingScrolloffsets: function(element, x, y) {
    var offsetcache = Element.cumulativeScrollOffset(element);

    this.xcomp = x + offsetcache[0] - this.deltaX;
    this.ycomp = y + offsetcache[1] - this.deltaY -
document.viewport.getScrollOffsets()[1];
    this.offset = Element.cumulativeOffset(element);

    return (this.ycomp >= this.offset[1] &&
            this.ycomp <  this.offset[1] + element.offsetHeight &&
            this.xcomp >= this.offset[0] &&
            this.xcomp <  this.offset[0] + element.offsetWidth);
  }

On Jan 10, 8:28 am, Ed209 <[EMAIL PROTECTED]> wrote:
> I have a drop box <div> with position:fixed at the bottom of the
> browser window. In cases where the web page is quite long, and I need
> to scroll, I can no longer drag items into the drop box because it has
> scrolled up along with the page.
>
> The visible drop box remains at the bottom of the page, but the
> 'droppable' area moves. this issue has been documented several times
> but there doesn't seem to be a solution. Has anyone encountered this
> before? Any solutions? V1.8.1 Prototype 1.6.0.1
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