I've noticed that since I down/upgraded to Windows 10 I'm getting very small head-set tracking glitches. At least I think they're tracking glitches - there are very small brief judders on occasion. For the most part VR works great, but now I've noticed these little glitches it's got super annoying. I don't think its supersampling as it happens in games where I don't supersample. I've turned off all the sleep modes/power saving for USB, and tried moving the sensors around the various USB ports.
I do notice slight glitches in tracking when games are loading, but it's fine once in-game, so maybe it's I/O related? I'd check if your storage driver- it could be using a default Windows version instead of the latest vendor driver.