I found 2 issues with sortable if it is in relative container which is in overflow: scroll.
Look at this jsfiddle demo. Scroll down and drag one of the items there. You will see that after you click on the item, the helper jumps to the bottom by value of scroll position. It happens only at first drag.
After some code inspection I've found place where it happens and possible solution.
_mouseStart method in sortable module calcaulates parent offset at the beginning (calling _getParrentOffset method). Interesting code fragment from this method:
left: event.pageX - this.offset.left,
top: event.pageY - this.offset.top
parent: this._getParentOffset(), //HERE
this.cssPosition = this.helper.css("position");
Look at the end of this snippet and look at _getParentOffset code below. this.cssPosition i set up after _getParentOffset call. Interesting thing is that _getParentOffset had code which resolves problem with nested scrolls and relatives but it relys on this.cssPosition property (which is not set at first time)