Same here but with NVidia GTX 960 and it happens in Dota 2 VR.
Can confirm it affects me too in steamvr home, Nvidia 384.69 on Mint 18.2, GTX 1060 + Ryzen 7 1800X
To confirm, this doesn't happen in other non-Valve apps like Serious Sam?
I don't own Serious Sam so unable to check, I've been trying to get UE4 to work both as editor and as crosscompiled game from windows, and so far no luck with that. I get the feeling nvidia's driver is a bit shaky, just updated to 384.90 and steamvr home no longer randomly freezes but still have the stutters, feels less frequent though.
I'm relatively sure I haven't seen specifically this in any other application.
I'm seeing this happen with my RX 580. Only in SteamVR Home. Using Mesa 19.1.6.
I see this happening a lot on my rx 5700 XT. Mesa 19.3.0-devel (git-ff6e148a3d) (LLVM 10.0.0), kernel 5.4rc4. Neither kernel nor Mesa version matter for this problem, only the refresh rate seems to have an effect (higher refresh rate - higher flickering rate). SteamVR version is 1.8.17. It happens predominately on the right eye, although the left eye isn't completely spared as well.
The frame timing graph has lots of sort of "spikes" with red marked frames in between, like here:

Sometimes it just reprojects through for a while and then it works fine.
Using the command from #82 cuts the frame time by a third or so and makes all flickering disappear. There is some frames it seems to reproject for no reason at all though:

Nothing extracted yet.
RX 480, latest radv. It's been happening for a while.
What it looks like: https://www.youtube.com/watch?v=HOmTLkxUgnw
It looks like when reprojection starts/stops there is a single frame where it renders the world from a position that is quite a bit off from the actual position. Possibly the center of the playspace? (I have a standing setup configured, no roomscale).
When looking up/down towards the left side, there is just the right amount of stuff on the screen so reprojection starts and stops. All is good when looking at the right side because it's running well enough without reprojection there.