message box not displayed

Revision 1
We have C# web application ,on button click event we do a data load process using stored procedure which runs for 3 hours,after the procedure finish loading we display a message box using code

ScriptManager.RegisterStartupScript(this, this.GetType(), Guid.NewGuid().ToString(), scriptString, true); and turn radiobuttion.SelectedIndex = 2;

if the procedure completes in 1 hour things are fine,if it runs for more than 2 hours ,the page turns unresponsive(message box not displayed, radio button not changed),i tried debugged the code, the code process through all lines and completes with no display,can anyone help