Basically when you link a model popup to a panel and run it you will notice that for a brief second (longer depending on the amount on your page) the panel will be visible then hidden.
Anyway, to stop the panel from showing simply add a style='display:none' attribute to the panel e.g.:-
<asp:Panel ID="pnlDontShowMe" RunAt="server" style="display:none">This will sort out the problem!
Hope this helps!