i3 user here.
I’ve had this problem with my LUKS password (no typing cursor displayed, password dots pixelate-fade in and out) since before using i3. I am on R4.1 and used the default, XFCE4, before i3. It didn’t bother me since the delayed password dot appearances could even be construed as security feature (— not a bug!).
I did not have this problem once I’d logged in to XFCE, though, and nor on my previous OS. This problem did immediately occur, however, after logging into i3. It stuck out then, but I don’t notice it as much now, as I’ve gotten used to it. In my brief and still preliminary experimentation with
xmonad on Qubes, I can say that I haven’t seen this problem yet.
Regardless, it looks like whatever is handling the GUI is rendering the VMs’s GUIs line by line, block by block. I don’t know how the GUI renderer works, but it might be having issues with i3, since XFCE worked fine. Maybe i3 has a different process for treating windows? The Qube Manager and my Firefox bookmarks have a lot of this weird effect. My laptop is recent and has enough RAM and CPU (hardware, maybe not software-allocated?) to not be a bottleneck.
Maybe someone who knows about how the VMs’s GUIs are rendered and how that information is passed to the window manager could comment?