If you are using runtime css, you would have come across the problem of the default theme color appearing for a fraction of a second before switching to the new theme. This would again depend on where you are trying to load the new theme. In case, its loaded only once at the time of initialization of the application, the following steps would fix the issue:
1. Call StyleManager.loadStyleDeclarations(url) in the preinitialize handler for your <mx:Application>
2. Make sure that your <mx:Application> has a creationPolicy=”none”.
3. When, the StyleEvent.COMPLETE event is triggered after the call to loadStyleDeclarations, then, you can call createComponentsFromDescriptors(). This method will create all of the children of the container that it is called on.
In case, your application requires that the theme be changed on user interaction or while the application is already running, you will have to override the styleChanged() method of the application to stop its background color from getting reset in the process of loading the style declarations by the StyleManager. Here is what you do:
Simply add
override public function styleChanged(styleProp:String):void {}
inside the script tags of the main application.

I am not sure what this article is all about. Are we talking of wordpress theme here?
No dear! its about flex themes.