Hi Ghalib,
Sorry I don't have any advice on this one as I've never used the ModalPopupExtender, probably google is your best bet to find an answer on this one, only thing I might try is wrapping it in an UpdatePanel.
Myself when I want a modal dialog I use a real .aspx page for the dialog and I open it with colorbox to make it modal. If you make a link to a page with the class="cblink" it will open it in a colorbox modal.
Maybe someone else has used this and has some ideas but I have no experience with that particular control.
Best,
Joe