I've had time to do a test now with a similar setup. Many thanks for all the details above.
Here's how I had things configured:
- two monitors, primary on the right, secondary on the left.
- resolutions were both 3840x2160 at 200% desktop scaling/DPI. (Not 1920x1200 but, knowing both screens are the same resolution and scaling is the main thing, as mixtures can complicate things more. If you're at 100% scaling then you're also not going to be triggering any DPI-related issues.)
- Elite Dangerous running on primary (right) monitor, borderless, at native resolution.
- Taskbar on primary (right) monitor (i.e. under the game).
- "Show taskbar on all displays" is off. DisplayFusion is not installed.
- GTX 1080ti with 417.71 drivers (haven't tried 418.91, but it sounds like you tried with this version as well).
Graphics settings in-game:
(I tried all three mouse cursor settings in case they were somehow related, but they didn't seem to matter.)
Video where I open Opus windows on both monitors and change folders in them:
As you can see there, no problems with flickering.
Windows were opened by double-clicking the desktop on the left (secondary) monitor.
Re DisplayFusion and similar tools, you typically have to uninstall them and reboot to remove them entirely. Just closing down the front-end part of them won't always render them inert.
It's not definite that it is DF or anything similar, but it's the first thing I would rule out myself.
Another possibility is Opus is doing something which causes the taskbar to want to alert you. If the taskbar wants to appear for some reason then it might make some games flicker when it does. But it's not normal for the taskbar to want to alert you just because a window has opened, unless it has problems giving the window focus, or there's some other condition. Even less so when just changing folders.
The Opus update checker might be displaying a notification, which could appear on top of the game (depending on Windows notification settings).
I have noticed that notifications, even ones for achievements triggered by the games themselves, can cause some games to flicker multiple times as the notifications appear and disappear lately. That seemed like a new OS-level bug in a recent Windows 10 update, or perhaps a recent NVidia driver. I noticed it with Forza Horizon 4 recently and its own achievement popups. (No involvement from Opus there at all, but it could be the same underlying problem in the OS/driver. I'm sure notification popups did not do that until recently, as Forza Horizon 3 triggered them frequently and did not ever flicker like that. I don't know if it relates to what you're seeing as there's also no reason Opus would be showing you notifications when just changing folders, and presumably you'd notice the notifications appearing if it was.)