I think this is caused by the vertical offset of the jScrollPaneContainer DIV, by no means do I guarantee this fix but it seems to work...for me at least:-)...
Line 64 of jScrollPane.js dated 2008-02-17 is: var currentScrollPosition = settings.maintainPosition ? $this.offset({relativeTo:jQuery(this).parent()[0]}).top : 0; You can get the vertical offset of jScrollPaneContainer with: jQuery(this).parents(".jScrollPaneContainer").offset().top So if you take that away from the currentScrollPosition maintainPosition seems to work: var currentScrollPosition = settings.maintainPosition ? $this.offset({relativeTo:jQuery(this).parent()[0]}).top - jQuery(this).parents(".jScrollPaneContainer").offset().top : 0; hope that helps