Flash is not working on my Surface RT on either IE, whether it's the one on the Start menu or the one on the desktop. I have gotten the most recent update to it and it is enabled. I even added the two test websites to the compatibility list. Nadda.
One of the reasons I wanted this was that flash is supposed to work. There are other, more affordable tablets, that work as well as, if not better, than this one at this moment. Combine that with sometimes working, sometimes not touch cover and it has been
a frustrating experience. Better yet, when the touch cover does respond, if you need the on-screen keyboard for any reason after that, you have to remove the touch cover. Folding it back doesn't allow that functionality, which at times, is very necessary.
Flash is already part of your Surface system. However, it only works with web sites Microsoft has white listed, i.e. deemed safe. With a little searching, you can find a way to amend the white list to include your preferred site.