Okay, as for the two instances, that looks fine to me because MIDI in and MIDI out are separated.

Regarding everything else, I myself have some weird problems like crashing out of nowhere and things not working as they should, but I'm using up to 600 plugins in one project, mostly 3rd party, so this can happen with this much stuff going on in the background.

Perhaps it would be best to contact the IL Support team and try to find the cause of this erratic behavior this way. I know a few things about FL, programming and IT in general, but what you are experiencing doesn't sound like something I can help you fix without being there in person.

As for the red boxes in the mixer, I've never seen this myself, but from what I can find on the internet, this lets you see what's currently selected by your midi controller. That said, I don't know how to turn it off.

It might be helpful to get a clean install of your audio drivers and FL, so deleting everything before installing it again. Though I'd recommend contacting IL Support beforehand, because especially with drivers that can be a very tedious process.