update panel with popup window is not working

Hi All,
 I have a .aspx page which is being opened with window.open() method. I have a scriptmanager and a update panel in it. In update panel I have a search control and two grids. 
When ever I am trying to do any postback, say seach button click from search control and any other button on the page I am getting below java script error.
Line: 513
Error: Sys.WebForms.PageRequestManagerParserErrorException: The message received from the server could not be parsed. Common causes for this error are when the response is modified by calls to Response.Write(), response filters, HttpModules, or server trace is enabled. Details: Error parsing near '<base target="_self"'.

To Solve the error, I have to register each postback creating control with script Manager like this: 
   ((ScriptManager)this.FindControl("ScriptManager1")).RegisterPostBackControl(ctr);
Above work arrond ...