Hello Nishanth,
You have stated that you are using Q1 2009, but the server-side RadAlert() method is available since Q1 2011, so I am assuming that you are using the current version and not the old one.
This is the first time such behavior is reported and I was not able to reproduce it with the provided information. You can find my test page attached and here is a video from my experiment: http://screencast.com/t/FSFcVrrx.
I assumed that you are using AJAX on the page and thus I simulate a long AJAX request in the page_Load method. I have set up a Loading Panel to hide the contents of the page during the callback, yet as soon as it is done the contents are displayed again.
Are you experiencing this behavior only under certain browsers? Am I missing something? Can you reproduce your issue with my page? If so please modify it accordingly and send it back so that we can investigate it further.
All the best,
Marin
the Telerik team
Consider using RadControls for ASP.NET AJAX (built on top of the ASP.NET AJAX framework) as a replacement for the Telerik ASP.NET Classic controls, See the product support lifecycle here.