Sounds like an extremely cool setup!
Though I wouldn't be surprised if it's a little fragile, too.
I'd check some things to make sure it's not your system. Your specs are impressive, but 3 times 5k is something that's still very new tech.
TB3 is notoriously unreliable or at least TB3 hubs are. I have some mistrust in the whole stack.
It might be that you've never observed it with TB10, because back then the graphics card was still doing fine.
My own graphics card started having trouble pushing monitor 2 and 3 at the same time, and I recently got the whole CPU/GPU and Mainboard unit replaced under Lenovo's warranty. I also observed flickering there (not quite like that and not triggerable by TheBrain 11).
I'd at least reinstall TB10 and check if it doesn't show the same behaviour today that it didn't show back then.
It's definitely not impossible that it's the software's fault, but it's somewhat unlikely from my understanding.
[as for assuming it's not your hardware getting old]
How many TheBrain-Windows are open, are they all on one screen, multiples or are they spanning over them?
Depending on that I might be able to try to do a similar thing on my 3-screen setup. This is on Windows 10 and barely a third of your pixels,
it's not like there's many people with a triple monitor setup to begin with and we gotta stick together here 🙂
One of my monitors is also connected to TB3. In my experience though, TB handles multi monitor stuff and multiple instances reasonably well.
Only thing that might give it pause is multiple virtual destkop, where I managed to provoke a crash a couple of times, but it doesn't seem related:
At the moment I still consider myself in the "setup" phase of using my own Brain and barely have need for using three monitors with it at once, but I'll be able to push this to the limits soon.