This problem doesn't occur in master because the styles have changed.
Steps to reproduce:
- select 2 columns layout
- set column-2 with login portlet
- set column-2 with bookmarks portlet
- drag & drop bookmarks portlet below login portlet. Drop it 30 px below the end of login portlet
- when the mouse button is released, bookmarks portlet is shown on top of column-1
This happens because the calculation of the position is made in relation of the column-1 container.
Due the display css property of the column, column-1 has exactly the same height of column-2. This is the main cause of the behaviour, because the position is processed using the column height.