I know this is an old post, but I am facing the same issue when calling my .Net Web Service methods.
If I test the calls from IIS is pretty fast (average 6 seconds) for a complicated call. However, from Flex this time is doubled. I used flash.util.getTimer() method to calculate the time elapsed from when i make the web service call until I receive a response back. So, not GUI rendering is part of this measurement.
I am also using the proxy classes that Flex auto generated for me when connected to my web service.