While using update panel and script manger, you need to register script to script manger and not to the page.
look below code.
Dim s2 As String = "<SCRIPT language='javascript'>"
s2 = s2 & "alert('Please Enter Quantity');"
s2 = s2 & " </script>"
ScriptManager.RegisterStartupScript(Me, Me.GetType, "savedt", s2, False)