Hi Geoffrey,
The problem occurs only when the windows are modal.
For some reason, trying to simplify my code I can't manage to make my window modal anymore (or even make the close button work). I'm not going to send my big real code, it's a little too complex. The code below should theoretically reproduce the bug.
<cool:Window ID="WindowPopup1" runat="server" AnimateTarget="true" Modal="true" CloseAction="Hide" Width="600" Height="300" Resizable="true">
<Content>
<asp:UpdatePanel ID="UpdatePanelQueryBuilderKill" runat="server" UpdateMode="Conditional">
<ContentTemplate>
<asp:DropDownList ID="DropDownList1" runat="server">
</asp:DropDownList>
</ContentTemplate>
</asp:UpdatePanel>
</Content>
</cool:Window>
<cool:Window ID="WindowPopup2" runat="server"
AnimateTarget="true" Modal="true" CloseAction="Hide" Width="600"
Height="300" Resizable="true">
<Content>
<asp:UpdatePanel ID="UpdatePanelQueryBuilderKill" runat="server" UpdateMode="Conditional">
<ContentTemplate>
<asp:DropDownList ID="DropDownList1" runat="server">
</asp:DropDownList>
</ContentTemplate>
</asp:UpdatePanel>
</Content>
</cool:Window>
Hope you manage to reproduce it. I'm using IE6