Have you had midi going into the OT? That can mess things up if your not completely on top of it…
Most often strange things with OT in the first few months are something you did with the project and its sneaky to find or realize what you did, not always though…
I’ve had zero midi issues and three years in my OT doesn’t really give me any trouble, it works exactly the same everytime… I fully absolutely trust it for live, it’s never glitched, froze, or done anything weird that wasn’t my fault… When learning it though I would mess it up and think it’s buggy, but every time I figured out what I did…
There’s a few minor bugs but once you find them they’re easily avoidable… And those have to do with track recorders/pickups//parts/scenes, nothing you’ve mentioned…
Again mk1 1.25 H though, but still, just trying to give you some hope…
I never have to do an empty reset either, although I do do it after an OS upgrade just for good measure, also always save projects under the new OS and reload…
And midi has been exactly the same for many, many years… There shouldn’t be any kind of new/old gear midi conflicts… Do have transport send enabled?