I thought I would jump in here as I think I have seen something similar in my testing with the 5500.
In running a speedtest that not only measures the speed but how long it takes for packets to come and go in a stream, I noticed that with the speed(stream) boost enabled, an upload will stream for 2 seconds, pause for 2 seconds then finish the rest of the test. I will post a screenshot of this when I get home. If I take speed(stream) boost off I do not get the delay.
I have an XBone (wired) and I too, have the 2% loss both with the stream boost on or off. I thought it was my internet, but now I am wondering if it is the router.
Edit: corrected terminology