When adding a new master page and moving around the delegate control with control id "SmallSearchInputBox" then you can experience an error that will appear either when editing columns or adding new workflows to your library or list.

The Error will be something like this:
"System.Web.UI.ViewStateException: Invalid viewstate.    Client IP: fe80::c07f:6fa4:e122:c0ef%11   Port: 1250   User-Agent: Mozilla/5.0 (compatible; MSIE 9.0; Windows NT 6.1; WOW64; Trident/5.0)   ViewState: /wEWCAKb9uO+DgKyx+vACgLNsInWBALjvdeFDwLWo p/GDwKMoP7ICwLU2oa9DQKizt7UDUIZl5wTN 95E6rz74k/p8OiMR4oZ   Referer: http://[servername]/layouts/AddWrkfl.aspx?List={FC0 22FA4-C4A2-42C2-AC01-8C1F97C22534}   Path: /layouts/CstWrkflIP.aspx"

The reason for this is simply that when posting the form in that particular application page, the page require(for some reason) that the search box should not render because if it do it will throw the "Invalid Viewstate" error. So you should not take the delegate control out of it's ContentPlaceHolder which is the "PlaceHolderSearchArea" because the application page uses this to make sure that the delegate control does not render on this particular state and therefore avoids the error. So if you want to move the search box, move the ContentPlaceHolder as well.

The downside is of course that you don't have 100% control of when the search box should be shown or not. If you have build an own custom delegate that you want to be included in all pages you will be 100% that this will be the case in all pages as any page can change the content in the ContentPlaceHolder.