I was facing the same problem and I figured that it was due a CSS style issue.
<body>
<form id="form1" runat="server">
<asp:ScriptManager ID="ScriptManager1" runat="server">
</asp:ScriptManager>
<util:FrameworkWebPartManager ID="webpartManagerMain" runat="server" onwebpartadded="webpartManagerMain_WebPartAdded" />
<div class="container">
<!-- Web Parts -->
</div>
</body>
Style Sheet
.container
{
padding: 0px;
margin-top: 5px;
margin-right: auto;
margin-bottom: 0px;
margin-left: auto;
/* position: relative; */ /* Got rid of this */
font-family: Arial, Helvetica, sans-serif;
font-size: 12px;
color: #333333;
height: 550px;
width: 990px;
}
The style "container" was setting the "position" to "relative" which caused the problem for me. Removing it made the drap and drop work just fine. Hope this helps !