Hi Konstantin Dikov & Radoslav,
After long time, I've discovered the issue. The issue was neither in the telerik controls nor in Ajax Control toolkit.
I improved error logs in my application and found that one of our custom http handler which was used for SQL Injection protection was blocking request of telerik and ajax toolkit handlers.
In this handler, we are blocking characters like xp_c, xp_d, delete etc. When telerik we resource was generating query string which is random, some time it contains characters which are in our black list characters in our custom handler and was blocked.
Here is the example : http://www.mysite.com/Telerik.Web.UI.WebResource.axd?jdfkgfdjgfdgxp_crtertg
I changed this handler to skip telerik resources for scanning and issue is resolved.
Thank you very much for your kind support.