Currently I'm working on a project using C# and with a Flash front end. The transparency issue i have overcame and what is needed is in visual studio on the form transparency key which is near the bottom of the properties - need to set that as a color such as green and when the color is shown print screen then open up photo shop paste the image get the correct color of the green and set that color as the background in the flash movie. Also in visual studio set the form mode so it does not have title bar close or minimize box. Right now my app sends fs commands to c# to minimize close, and operations that c# needs to perform and all the interface is flash based and resizable. The flash uses xml for some of the interface related information and c# will do the brunt of the work of the app. The app now has a pretty cool look and feel and i have seen nothing yet like it. So far when the program runs it will have a transparent look for the alpha per pixel of 0% or 100% although not semi transparent say 50% which i would love to find an answer to that. In visual studio on the form if you set the transparency of the form to other than fully opaque it will mess up the look of the flash and display the color green semi transparent. As well on the photoshop side you want to make sure that the .png's used on the edges of the graphics are either fully opaque other wise it will display a green edge around the app when ran.
I'm not a pro on c#, but if anyone found this useful or even not i would greatly appreciate any information on sending data from c# to flash.