I assume that you are using the following sample from our online demos to give custom looks to your docks: http://demos.telerik.com/aspnet-ajax/dock/examples/portalpage/defaultcs.aspx. In this demo we are using CSS id selectors to apply unique styles to every dock. When the docks are placed in a "normal" page the ClientIDs of the docks are the same as the server IDs. So if we have a dock with ID="Weather" the following style will be successfully applied: #Weather{background:#f1eee1;}. However if the same dock is in a content page of a MasterPage (or in a WebUserControl) the styles will not be applied because this time the dock has different ClientID. The ClientId will look something like XXX_XXXX_Weather and the same style should be modified: #XXX_XXXX_Weather{background:#f1eee1;}. You can use IE Dev toolbar for IE browsers or Firebug addin for Firefox to find the correct ClientID (as shown in the attached screenshot).
A different way to apply the same styles is to replace the id selectors with class selectors and set the custom CSS class to the CssClass property of the respective dock.