While working through a website using master pages and content placeholders one thing that has come to my attention is that controls inside the content placeholders are now named differently. It is obvious that the client name of the control would be different, however, controls that use naming convention of this.ClientID might not function properly now.
Even with the atlas:updatepanel if you have any controls inside it, it is suppose to automatically do partial rendering (provided script manager is set for partial rendering), but this does not function correctly if it is placed inside a content placeholder. You can force it by setting up a trigger manually, but you are out of luck if you are trying to work with controls inside gridview or datalist etc. (Try it without master pages)
Also, what I have found is, any control programmed conventionally in asp.net 1.1 that uses this.ClientID and javascript to refer to the control, might not function properly. Work around for now is to either use this.ID or modified version of this.ClientID so it matches whats displayed in the browser source code. Again, it’s a hit and trial to get it to match and be unique.
If anyone has run into the same problem, and has a work around then I would like to hear about it.