jquery-ui-droppable-iframe-fix.js

// Create new object to cache iframe offsets
$.ui.ddmanager.frameOffsets = {};
 
// Override the native `prepareOffsets` method. This is almost
// identical to the un-edited method, except for the last part!
$.ui.ddmanager.prepareOffsets = function (t, event) {
    var i, j,
        m = $.ui.ddmanager.droppables[t.options.scope] || [],
        type = event ? event.type : null, // workaround for #2317
        list = (t.currentItem || t.element).find(":data(ui-droppable)").addBack(),
        doc, frameOffset;
 
    droppablesLoop: for (i = 0; i < m.length; i++) {
 
        //No disabled and non-accepted
        if (m[i].options.disabled || (t && !m[i].accept.call(m[i].element[0], (t.currentItem || t.element)))) {
            continue;
        }
 
        // Filter out elements in the current dragoged item
        for (j = 0; j < list.length; j++) {
            if (list[j] === m[i].element[0]) {
                m[i].proportions().height = 0;
                continue droppablesLoop;
            }
        }
 
        m[i].visible = m[i].element.css("display") !== "none";
        if (!m[i].visible) {
            continue;
        }
 
        //Activate the droppable if used directly from draggables
        if (type === "mousedown") {
            m[i]._activate.call(m[i], event);
        }
        
        // Re-calculate offset
        m[i].offset = m[i].element.offset();

        // Re-calculate proportions (jQuery UI ~1.10 introduced a `proportions` cache method, so support both here!)
        proportions = { width: m[i].element[0].offsetWidth, height: m[i].element[0].offsetHeight };
        typeof m[i].proportions === 'function' ? m[i].proportions(proportions) : (m[i].proportions = proportions);
        
        /* ============ Here comes the fun bit! =============== */
 
        // If the element is within an another document...
        if ((doc = m[i].document[0]) !== document) {
            // Determine in the frame offset using cached offset (if already calculated)
            frameOffset = $.ui.ddmanager.frameOffsets[doc];
            if (!frameOffset) {
                // Calculate and cache the offset in our new `$.ui.ddmanager.frameOffsets` object
                frameOffset = $.ui.ddmanager.frameOffsets[doc] = $(
                    // Different browsers store it on different properties (IE...)
                    (doc.defaultView || doc.parentWindow).frameElement
                ).offset();
            }
           
           //get iframe scroll offsets
            var frameScrollTop = doc.documentElement.scrollTop || doc.body.scrollTop;
            var frameScrollLeft = doc.documentElement.scrollLeft || doc.body.scrollLeft;
            
            // Add the frame offset to the calculated offset
            //append offsets to drag drop position
            m[i].offset.left += frameOffset.left - frameScrollLeft;
            m[i].offset.top += frameOffset.top - frameScrollTop;
        }
    }
};

if the user starts to scroll in the iframe then the position of the drag drop items get changed based on top=0 and left=0.
The above code hopefully mends that problem.

Did your fix end up solving this issue?