The last update I have is dated Feb 20. I did not have Amazon on my compatibility list. It did not work. I then added it to the list, but it did not work either. Like you I have three tracking protection lists active. There was nothing in particular that I was/ am interested in. I was just trying Prime/ Instant Video out. Nothing works - in terms of watching films, TVs shows etc.
That's annoying as all get-out. I'm assuming you're getting the "you need to update your Flash player"-type error?
According to Adobe - Flash Player , my Surface 2 has Flash 22.214.171.124, and I'm streaming some random things fine. (Meanwhile, my desktop PC with Opera 12.x as my main browser and the latest Flash 126.96.36.199 is getting errors from Amazon again, and clearing cookies didn't work. Works in Firefox and probably IE at least.)
My last Win patches included the optional KB2919394, and I haven't installed anything after Feb 18 if there have been other updates. I have no idea if anything external (like networking stuff) can affect Ama streaming as well. This might be something to post on the MS boards. It's strange because the Surface RT experience should be pretty consistent across users, unlike your average PC.