In the issueThis issue is described. The title was copied since it covers this issue aswell.
When I apply a custom region style (eg. List) and enable Panels IPE as Panels renderer, the problem occur as soon as the second element is added to a region. (Look at screenshot)
In the JS function DrupalPanelsIPE.createSortContainers the .panels-ipe-sort-container wrapper is attached twice if there is an extra wrapper in the region style.
The class "panels-ipe-portlet-marker" on "panels-ipe-placeholder" dosen't do anything so I believe that it's safe to remove it.
For some reason I haven't figured out. The extra wrapper in the default pane style is also outcommented. http://drupalcode.org/project/panels.git/blob/2bdcf24e4248674a0e22b988ec...